1 Calculating error rates.

I wrote the function ‘create_matrices()’ to collect mutation counts. At least in theory the results from it should be able to address most/any question regarding the counts of mutations observed in the data.

devtools::load_all("errRt")

## Loading errRt

## Loading required package: dplyr

## 
## Attaching package: 'dplyr'

## The following object is masked from 'package:hpgltools':
## 
##     combine

## The following object is masked from 'package:Biobase':
## 
##     combine

## The following objects are masked from 'package:BiocGenerics':
## 
##     combine, intersect, setdiff, union

## The following objects are masked from 'package:stats':
## 
##     filter, lag

## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union

## Loading required package: tidyr

triplets <- create_matrices(sample_sheet="sample_sheets/all_samples.xlsx",
                            ident_column="identtable", mut_column="mutationtable",
                            min_reads=3, min_indexes=3, min_sequencer=10,
                            min_position=24, prune_n=TRUE, verbose=TRUE)

## Starting sample: 1.

## Reading the file containing mutations: preprocessing/s1/step4.txt.xz

## Reading the file containing the identical reads: preprocessing/s1/step2_identical_reads.txt.xz

## Removing any differences before position: 24.

## Before pruning, there are: 1156535 reads.

## After position pruning, there are: 1037310 reads.

## Removing any reads with 'N' as the hit.

## Before N pruning, there are: 1037310 reads.

## After N pruning, there are: 1021066 reads.

## Gathering information about the indexes observed, this is slow.

## Before read pruning, there are: 1742743 indexes.

## After read pruning, there are: 838158 indexes.

## Removing indexes with fewer than 3 indexes.

## Before index pruning, there are: 1021066 changed reads.

## Before index pruning, there are: 4681501 identical reads.

## After index pruning, there are: 532571 changed reads.

## After index pruning, there are: 3663814 identical reads.

## Gathering identical, mutant, and sequencer reads/indexes.

## Counting by direction.

## Counting by string.

## Subsetting based on mutations with at least 3 indexes.

## Counting by reference position.

## Counting by identity string.

## Counting by reference nucleotide.

## Counting by product nucleotide.

## Counting by mutation type.

## Counting by transitions/transversion.

## Counting strong/weak.

## Counting insertions by position.

## Counting insertions by nucleotide

## Counting deletions by position.

## Counting deletions by nucleotide.

## Starting sample: 2.

## Reading the file containing mutations: preprocessing/s2/step4.txt.xz

## Reading the file containing the identical reads: preprocessing/s2/step2_identical_reads.txt.xz

## Removing any differences before position: 24.

## Before pruning, there are: 3421203 reads.

## After position pruning, there are: 1758479 reads.

## Removing any reads with 'N' as the hit.

## Before N pruning, there are: 1758479 reads.

## After N pruning, there are: 1732605 reads.

## Gathering information about the indexes observed, this is slow.

## Before read pruning, there are: 1263563 indexes.

## After read pruning, there are: 694479 indexes.

## Removing indexes with fewer than 3 indexes.

## Before index pruning, there are: 1732605 changed reads.

## Before index pruning, there are: 5230976 identical reads.

## After index pruning, there are: 874781 changed reads.

## After index pruning, there are: 4834367 identical reads.

## Gathering identical, mutant, and sequencer reads/indexes.

## Counting by direction.

## Counting by string.

## Subsetting based on mutations with at least 3 indexes.

## Counting by reference position.

## Counting by identity string.

## Counting by reference nucleotide.

## Counting by product nucleotide.

## Counting by mutation type.

## Counting by transitions/transversion.

## Counting strong/weak.

## Counting insertions by position.

## Counting insertions by nucleotide

## Counting deletions by position.

## Counting deletions by nucleotide.

## Starting sample: 3.

## Reading the file containing mutations: preprocessing/s3/step4.txt.xz

## Reading the file containing the identical reads: preprocessing/s3/step2_identical_reads.txt.xz

## Removing any differences before position: 24.

## Before pruning, there are: 4309681 reads.

## After position pruning, there are: 1564155 reads.

## Removing any reads with 'N' as the hit.

## Before N pruning, there are: 1564155 reads.

## After N pruning, there are: 1532016 reads.

## Gathering information about the indexes observed, this is slow.

## Before read pruning, there are: 887982 indexes.

## After read pruning, there are: 465046 indexes.

## Removing indexes with fewer than 3 indexes.

## Before index pruning, there are: 1532016 changed reads.

## Before index pruning, there are: 3583390 identical reads.

## After index pruning, there are: 783358 changed reads.

## After index pruning, there are: 3332425 identical reads.

## Gathering identical, mutant, and sequencer reads/indexes.

## Counting by direction.

## Counting by string.

## Subsetting based on mutations with at least 3 indexes.

## Counting by reference position.

## Counting by identity string.

## Counting by reference nucleotide.

## Counting by product nucleotide.

## Counting by mutation type.

## Counting by transitions/transversion.

## Counting strong/weak.

## Counting insertions by position.

## Counting insertions by nucleotide

## Counting deletions by position.

## Counting deletions by nucleotide.

## Working on miss_reads_by_position.

## Working on miss_indexes_by_position.

## Working on miss_sequencer_by_position.

## Working on miss_reads_by_string.

## Warning in order(as.numeric(rownames(matrices[[t]]))): NAs introduced by
## coercion

## Working on miss_indexes_by_string.

## Warning in order(as.numeric(rownames(matrices[[t]]))): NAs introduced by
## coercion

## Working on miss_sequencer_by_string.

## Warning in order(as.numeric(rownames(matrices[[t]]))): NAs introduced by
## coercion

## Working on miss_reads_by_ref_nt.

## Working on miss_indexes_by_ref_nt.

## Working on miss_sequencer_by_ref_nt.

## Working on miss_reads_by_hit_nt.

## Working on miss_indexes_by_hit_nt.

## Working on miss_sequencer_by_hit_nt.

## Working on miss_reads_by_type.

## Working on miss_indexes_by_type.

## Working on miss_sequencer_by_type.

## Working on miss_reads_by_trans.

## Working on miss_indexes_by_trans.

## Working on miss_sequencer_by_trans.

## Working on miss_reads_by_strength.

## Working on miss_indexes_by_strength.

## Working on miss_sequencer_by_strength.

## Working on insert_reads_by_position.

## Working on insert_indexes_by_position.

## Working on insert_sequencer_by_position.

## Working on insert_reads_by_nt.

## Working on insert_indexes_by_nt.

## Working on insert_sequencer_by_nt.

## Working on delete_reads_by_position.

## Working on delete_indexes_by_position.

## Working on delete_sequencer_by_position.

## Working on delete_reads_by_nt.

## Working on delete_indexes_by_nt.

## Working on delete_sequencer_by_nt.

## Skipping table: delete_reads_by_position

## Skipping table: delete_indexes_by_position

## Skipping table: delete_sequencer_by_position

## Skipping table: delete_reads_by_nt

## Skipping table: delete_indexes_by_nt

## Skipping table: delete_sequencer_by_nt

triplet_plots <- barplot_matrices(triplets)
summary(triplets)

##                      Length Class  Mode   
## samples               3     -none- list   
## reads_per_sample      3     -none- numeric
## indexes_per_sample    3     -none- numeric
## matrices             33     -none- list   
## matrices_by_counts   33     -none- list   
## normalized           33     -none- list   
## normalized_by_counts 33     -none- list

quintuplets <- create_matrices(sample_sheet="sample_sheets/all_samples.xlsx",
                               ident_column="identtable", mut_column="mutationtable",
                               min_reads=3, min_indexes=5, min_sequencer=10,
                               min_position=24, prune_n=TRUE, verbose=TRUE)

## Starting sample: 1.

## Reading the file containing mutations: preprocessing/s1/step4.txt.xz

## Reading the file containing the identical reads: preprocessing/s1/step2_identical_reads.txt.xz

## Removing any differences before position: 24.

## Before pruning, there are: 1156535 reads.

## After position pruning, there are: 1037310 reads.

## Removing any reads with 'N' as the hit.

## Before N pruning, there are: 1037310 reads.

## After N pruning, there are: 1021066 reads.

## Gathering information about the indexes observed, this is slow.

## Before read pruning, there are: 1742743 indexes.

## After read pruning, there are: 838158 indexes.

## Removing indexes with fewer than 5 indexes.

## Before index pruning, there are: 1021066 changed reads.

## Before index pruning, there are: 4681501 identical reads.

## After index pruning, there are: 532571 changed reads.

## After index pruning, there are: 3663814 identical reads.

## Gathering identical, mutant, and sequencer reads/indexes.

## Counting by direction.

## Counting by string.

## Subsetting based on mutations with at least 5 indexes.

## Counting by reference position.

## Counting by identity string.

## Counting by reference nucleotide.

## Counting by product nucleotide.

## Counting by mutation type.

## Counting by transitions/transversion.

## Counting strong/weak.

## Counting insertions by position.

## Counting insertions by nucleotide

## Counting deletions by position.

## Counting deletions by nucleotide.

## Starting sample: 2.

## Reading the file containing mutations: preprocessing/s2/step4.txt.xz

## Reading the file containing the identical reads: preprocessing/s2/step2_identical_reads.txt.xz

## Removing any differences before position: 24.

## Before pruning, there are: 3421203 reads.

## After position pruning, there are: 1758479 reads.

## Removing any reads with 'N' as the hit.

## Before N pruning, there are: 1758479 reads.

## After N pruning, there are: 1732605 reads.

## Gathering information about the indexes observed, this is slow.

## Before read pruning, there are: 1263563 indexes.

## After read pruning, there are: 694479 indexes.

## Removing indexes with fewer than 5 indexes.

## Before index pruning, there are: 1732605 changed reads.

## Before index pruning, there are: 5230976 identical reads.

## After index pruning, there are: 874781 changed reads.

## After index pruning, there are: 4834367 identical reads.

## Gathering identical, mutant, and sequencer reads/indexes.

## Counting by direction.

## Counting by string.

## Subsetting based on mutations with at least 5 indexes.

## Counting by reference position.

## Counting by identity string.

## Counting by reference nucleotide.

## Counting by product nucleotide.

## Counting by mutation type.

## Counting by transitions/transversion.

## Counting strong/weak.

## Counting insertions by position.

## Counting insertions by nucleotide

## Counting deletions by position.

## Counting deletions by nucleotide.

## Starting sample: 3.

## Reading the file containing mutations: preprocessing/s3/step4.txt.xz

## Reading the file containing the identical reads: preprocessing/s3/step2_identical_reads.txt.xz

## Removing any differences before position: 24.

## Before pruning, there are: 4309681 reads.

## After position pruning, there are: 1564155 reads.

## Removing any reads with 'N' as the hit.

## Before N pruning, there are: 1564155 reads.

## After N pruning, there are: 1532016 reads.

## Gathering information about the indexes observed, this is slow.

## Before read pruning, there are: 887982 indexes.

## After read pruning, there are: 465046 indexes.

## Removing indexes with fewer than 5 indexes.

## Before index pruning, there are: 1532016 changed reads.

## Before index pruning, there are: 3583390 identical reads.

## After index pruning, there are: 783358 changed reads.

## After index pruning, there are: 3332425 identical reads.

## Gathering identical, mutant, and sequencer reads/indexes.

## Counting by direction.

## Counting by string.

## Subsetting based on mutations with at least 5 indexes.

## Counting by reference position.

## Counting by identity string.

## Counting by reference nucleotide.

## Counting by product nucleotide.

## Counting by mutation type.

## Counting by transitions/transversion.

## Counting strong/weak.

## Counting insertions by position.

## Counting insertions by nucleotide

## Counting deletions by position.

## Counting deletions by nucleotide.

## Working on miss_reads_by_position.

## Working on miss_indexes_by_position.

## Working on miss_sequencer_by_position.

## Working on miss_reads_by_string.

## Warning in order(as.numeric(rownames(matrices[[t]]))): NAs introduced by
## coercion

## Working on miss_indexes_by_string.

## Warning in order(as.numeric(rownames(matrices[[t]]))): NAs introduced by
## coercion

## Working on miss_sequencer_by_string.

## Warning in order(as.numeric(rownames(matrices[[t]]))): NAs introduced by
## coercion

## Working on miss_reads_by_ref_nt.

## Working on miss_indexes_by_ref_nt.

## Working on miss_sequencer_by_ref_nt.

## Working on miss_reads_by_hit_nt.

## Working on miss_indexes_by_hit_nt.

## Working on miss_sequencer_by_hit_nt.

## Working on miss_reads_by_type.

## Working on miss_indexes_by_type.

## Working on miss_sequencer_by_type.

## Working on miss_reads_by_trans.

## Working on miss_indexes_by_trans.

## Working on miss_sequencer_by_trans.

## Working on miss_reads_by_strength.

## Working on miss_indexes_by_strength.

## Working on miss_sequencer_by_strength.

## Working on insert_reads_by_position.

## Working on insert_indexes_by_position.

## Working on insert_sequencer_by_position.

## Working on insert_reads_by_nt.

## Working on insert_indexes_by_nt.

## Working on insert_sequencer_by_nt.

## Working on delete_reads_by_position.

## Working on delete_indexes_by_position.

## Working on delete_sequencer_by_position.

## Working on delete_reads_by_nt.

## Working on delete_indexes_by_nt.

## Working on delete_sequencer_by_nt.

## Skipping table: delete_reads_by_position

## Skipping table: delete_indexes_by_position

## Skipping table: delete_sequencer_by_position

## Skipping table: delete_reads_by_nt

## Skipping table: delete_indexes_by_nt

## Skipping table: delete_sequencer_by_nt

quintuplet_plots <- barplot_matrices(quintuplets)
summary(triplets)

##                      Length Class  Mode   
## samples               3     -none- list   
## reads_per_sample      3     -none- numeric
## indexes_per_sample    3     -none- numeric
## matrices             33     -none- list   
## matrices_by_counts   33     -none- list   
## normalized           33     -none- list   
## normalized_by_counts 33     -none- list

2 Questions from Dr. DeStefano

I think what is best is to get the number of recovered mutations of each type from each data set. That would be A to T, A to G, A to C; T to A, T to G, T to C; G to A, G to C, G to T; and C to A, C to G, C to T; as well as deletions and insertions. I would then need the sum number of the reads that met all our criteria (i.e. at least 3 good recovered reads for that 14 nt index). Each set of 3 or more would ct as “1” read of that particular index so I would need the total with this in mind. I also need to know the total number of nucleotides that were in the region we decided to consider in the analysis. We may want to try this for 3 or more and 5 or more recovered indexes if it is not hard. This information does not include specific positions on the template where errors occurred but we can look at that latter. Right now I just want to get a general error rate and type of error. It would basically be calculated by dividing the number of recovered mutations of a particular type by sum number of the reads times the number of nucleotides screened in the template. As it ends up, this number does not really have a lot of meaning but it can be used to calculate the overall mutation rate as well as the rate for transversions, transitions, and deletions and insertions.

3 Answers

In order to address those queries, I invoked create_matrices() with a minimum index count of 3 and 5. It should be noted that this is not the same as requiring 3 or 5 reads per index. In both cases I require 3 reads per index.

3.1 Recovered mutations of each type

I am interpreting this question as the number of indexes recovered for each mutation type. I collect this information in 2 ways of interest: the indexes by type which are deemed to be from the RT and from the sequencer. In addition, I calculate a normalized (cpm) version of this information which may be used to look for changes across samples.

3.1.1 Mutations by RT index

This following block should print out tables of the numbers of mutant indexes observed for each type for the RT and the sequencer. One would hope that the sequencer will be consistent for all samples, but I think the results will instead suggest that my metric is not yet stringent enough.

knitr::kable(triplets[["matrices"]][["miss_indexes_by_type"]])

	s1	s2	s3
A_C	1294	4516	9418
A_G	728	14896	53401
A_T	235	2243	5053
C_A	9305	29486	34851
C_G	342	3848	10038
C_T	2133	18061	61965
G_A	1685	30686	37225
G_C	283	1683	3087
G_T	9630	12295	15293
T_A	222	5119	8532
T_C	854	4466	9521
T_G	1195	5972	11188

knitr::kable(triplets[["matrices"]][["miss_sequencer_by_type"]])

	s1	s2	s3
A_C	2381	18295	15010
A_G	659	7440	5942
A_T	224	3157	2592
C_A	1278	15254	11862
C_G	601	6072	4442
C_T	732	7343	5703
G_A	555	5215	4268
G_C	476	6334	5631
G_T	997	8701	7109
T_A	453	4280	3403
T_C	997	10482	8692
T_G	2471	27537	22137

knitr::kable(quintuplets[["matrices"]][["miss_indexes_by_type"]])

	s1	s2	s3
A_C	1281	4516	9418
A_G	708	14896	53401
A_T	215	2243	5053
C_A	9305	29486	34851
C_G	318	3844	10038
C_T	2129	18061	61965
G_A	1677	30686	37225
G_C	255	1679	3087
G_T	9627	12295	15293
T_A	198	5119	8532
T_C	842	4466	9521
T_G	1195	5969	11188

knitr::kable(quintuplets[["matrices"]][["miss_sequencer_by_type"]])

	s1	s2	s3
A_C	2374	18295	15010
A_G	651	7440	5942
A_T	202	3157	2592
C_A	1254	15254	11862
C_G	591	6072	4442
C_T	713	7343	5703
G_A	545	5215	4268
G_C	445	6334	5631
G_T	977	8701	7109
T_A	424	4280	3403
T_C	990	10482	8692
T_G	2458	27537	22137

Plots of this information

triplet_plots[["matrices"]][["miss_indexes_by_type"]]

triplet_plots[["normal"]][["miss_indexes_by_type"]]

quintuplet_plots[["matrices"]][["miss_indexes_by_type"]]

quintuplet_plots[["normal"]][["miss_indexes_by_type"]]

This suggests to me that this information needs to be normalized in some more sensible fashion. Thus the following:

3.1.2 Mutations by RT index, post normalization

The same numbers may be expressed in the context of the number of indexes observed / sample and/or as a cpm across samples. Thus in the first instance one can look at the apparent error rate for each sample, and in the second instance one may look for relative changes in apparent error rate across samples.

3.1.2.1 Rewriting the matrices as cpm to account for library sizes.

knitr::kable(triplets[["normalized"]][["miss_indexes_by_type"]])

	s1	s2	s3
A_C	46370	33886	36283
A_G	26088	111772	205727
A_T	8421	16830	19467
C_A	333441	221248	134263
C_G	12255	28873	38671
C_T	76435	135521	238720
G_A	60381	230253	143409
G_C	10141	12628	11893
G_T	345087	92256	58916
T_A	7955	38410	32869
T_C	30603	33511	36680
T_G	42822	44811	43102

knitr::kable(triplets[["normalized"]][["miss_sequencer_by_type"]])

	s1	s2	s3
A_C	201370	152319	155076
A_G	55734	61943	61390
A_T	18945	26284	26779
C_A	108085	127000	122553
C_G	50829	50554	45893
C_T	61908	61136	58921
G_A	46938	43419	44095
G_C	40257	52735	58177
G_T	84320	72442	73447
T_A	38312	35634	35158
T_C	84320	87270	89802
T_G	208982	229265	228709

knitr::kable(quintuplets[["normalized"]][["miss_indexes_by_type"]])

	s1	s2	s3
A_C	46162	33889	36283
A_G	25514	111781	205727
A_T	7748	16832	19467
C_A	335315	221267	134263
C_G	11459	28846	38671
C_T	76721	135532	238720
G_A	60432	230272	143409
G_C	9189	12599	11893
G_T	346919	92263	58916
T_A	7135	38414	32869
T_C	30342	33513	36680
T_G	43063	44792	43102

knitr::kable(quintuplets[["normalized"]][["miss_sequencer_by_type"]])

	s1	s2	s3
A_C	204233	152319	155076
A_G	56005	61943	61390
A_T	17378	26284	26779
C_A	107880	127000	122553
C_G	50843	50554	45893
C_T	61339	61136	58921
G_A	46886	43419	44095
G_C	38283	52735	58177
G_T	84050	72442	73447
T_A	36476	35634	35158
T_C	85169	87270	89802
T_G	211459	229265	228709

3.1.2.2 Rewriting the matrices by dividing by all indexes

This I think starts to address the later text in your query.

knitr::kable(triplets[["matrices_by_counts"]][["miss_indexes_by_type"]])

	s1	s2	s3
A_C	0.0015	0.0054	0.0112
A_G	0.0010	0.0214	0.0769
A_T	0.0005	0.0048	0.0109
C_A	0.0111	0.0352	0.0416
C_G	0.0005	0.0055	0.0145
C_T	0.0046	0.0388	0.1332
G_A	0.0020	0.0366	0.0444
G_C	0.0004	0.0024	0.0044
G_T	0.0207	0.0264	0.0329
T_A	0.0003	0.0061	0.0102
T_C	0.0012	0.0064	0.0137
T_G	0.0026	0.0128	0.0241

knitr::kable(triplets[["matrices_by_counts"]][["miss_sequencer_by_type"]])

	s1	s2	s3
A_C	0.0028	0.0218	0.0179
A_G	0.0009	0.0107	0.0086
A_T	0.0005	0.0068	0.0056
C_A	0.0015	0.0182	0.0142
C_G	0.0009	0.0087	0.0064
C_T	0.0016	0.0158	0.0123
G_A	0.0007	0.0062	0.0051
G_C	0.0007	0.0091	0.0081
G_T	0.0021	0.0187	0.0153
T_A	0.0005	0.0051	0.0041
T_C	0.0014	0.0151	0.0125
T_G	0.0053	0.0592	0.0476

knitr::kable(quintuplets[["matrices_by_counts"]][["miss_indexes_by_type"]])

	s1	s2	s3
A_C	0.0015	0.0054	0.0112
A_G	0.0010	0.0214	0.0769
A_T	0.0005	0.0048	0.0109
C_A	0.0111	0.0352	0.0416
C_G	0.0005	0.0055	0.0145
C_T	0.0046	0.0388	0.1332
G_A	0.0020	0.0366	0.0444
G_C	0.0004	0.0024	0.0044
G_T	0.0207	0.0264	0.0329
T_A	0.0002	0.0061	0.0102
T_C	0.0012	0.0064	0.0137
T_G	0.0026	0.0128	0.0241

knitr::kable(quintuplets[["matrices_by_counts"]][["miss_sequencer_by_type"]])

	s1	s2	s3
A_C	0.0028	0.0218	0.0179
A_G	0.0009	0.0107	0.0086
A_T	0.0004	0.0068	0.0056
C_A	0.0015	0.0182	0.0142
C_G	0.0009	0.0087	0.0064
C_T	0.0015	0.0158	0.0123
G_A	0.0007	0.0062	0.0051
G_C	0.0006	0.0091	0.0081
G_T	0.0021	0.0187	0.0153
T_A	0.0005	0.0051	0.0041
T_C	0.0014	0.0151	0.0125
T_G	0.0053	0.0592	0.0476

3.1.2.3 Rewriting the matrices by dividing by all indexes and cpm

I think this might prove to be where we get the most meaningful results.

The nicest thing in it is that after accounting for library sizes and total indexes observed, we finally see that the sequencer error is mostly consistent across all samples and mutation types – with a couple of notable exceptions.

By the same token, for the mutations which are identical for the sequencer, we have some which are decidedly different for the non-sequencer data. The most notable examples I think are A to G but _not G to A; and C to T.

knitr::kable(triplets[["normalized_by_counts"]][["miss_indexes_by_type"]])

	s1	s2	s3
A_C	0.0553	0.0404	0.0433
A_G	0.0376	0.1609	0.2962
A_T	0.0181	0.0362	0.0419
C_A	0.3978	0.2640	0.1602
C_G	0.0176	0.0416	0.0557
C_T	0.1644	0.2914	0.5133
G_A	0.0720	0.2747	0.1711
G_C	0.0146	0.0182	0.0171
G_T	0.7420	0.1984	0.1267
T_A	0.0095	0.0458	0.0392
T_C	0.0441	0.0483	0.0528
T_G	0.0921	0.0964	0.0927

knitr::kable(triplets[["normalized_by_counts"]][["miss_sequencer_by_type"]])

	s1	s2	s3
A_C	0.2403	0.1817	0.1850
A_G	0.0803	0.0892	0.0884
A_T	0.0407	0.0565	0.0576
C_A	0.1290	0.1515	0.1462
C_G	0.0732	0.0728	0.0661
C_T	0.1331	0.1315	0.1267
G_A	0.0560	0.0518	0.0526
G_C	0.0580	0.0759	0.0838
G_T	0.1813	0.1558	0.1579
T_A	0.0457	0.0425	0.0419
T_C	0.1214	0.1257	0.1293
T_G	0.4494	0.4930	0.4918

knitr::kable(quintuplets[["normalized_by_counts"]][["miss_indexes_by_type"]])

	s1	s2	s3
A_C	0.0551	0.0404	0.0433
A_G	0.0367	0.1610	0.2962
A_T	0.0167	0.0362	0.0419
C_A	0.4001	0.2640	0.1602
C_G	0.0165	0.0415	0.0557
C_T	0.1650	0.2914	0.5133
G_A	0.0721	0.2747	0.1711
G_C	0.0132	0.0181	0.0171
G_T	0.7460	0.1984	0.1267
T_A	0.0085	0.0458	0.0392
T_C	0.0437	0.0483	0.0528
T_G	0.0926	0.0963	0.0927

knitr::kable(quintuplets[["normalized_by_counts"]][["miss_sequencer_by_type"]])

	s1	s2	s3
A_C	0.2437	0.1817	0.1850
A_G	0.0806	0.0892	0.0884
A_T	0.0374	0.0565	0.0576
C_A	0.1287	0.1515	0.1462
C_G	0.0732	0.0728	0.0661
C_T	0.1319	0.1315	0.1267
G_A	0.0559	0.0518	0.0526
G_C	0.0551	0.0759	0.0838
G_T	0.1807	0.1558	0.1579
T_A	0.0435	0.0425	0.0419
T_C	0.1226	0.1257	0.1293
T_G	0.4547	0.4930	0.4918

3.1.3 Indels by RT index

The following blocks will repeat the above, but looking for insertions. This data does not observe sufficient deletions to make a proper count for them.

knitr::kable(triplets[["matrices"]][["insert_indexes_by_nt"]])

	s2	s3
A	25	382
C	23	70
G	31	89
T	51	221

knitr::kable(triplets[["matrices"]][["insert_sequencer_by_nt"]])

	s2	s3
A	3	8
C	23	24
G	14	16
T	0	3

knitr::kable(quintuplets[["matrices"]][["insert_indexes_by_nt"]])

	s2	s3
A	25	382
C	20	66
G	27	89
T	48	217

knitr::kable(quintuplets[["matrices"]][["insert_sequencer_by_nt"]])

	s2	s3
A	0	5
C	16	14
G	10	5

Plots of this information

triplet_plots[["matrices"]][["insert_indexes_by_nt"]]

triplet_plots[["normal"]][["insert_indexes_by_nt"]]

quintuplet_plots[["matrices"]][["insert_indexes_by_nt"]]

quintuplet_plots[["matrices"]][["insert_sequencer_by_nt"]]

quintuplet_plots[["normal"]][["insert_indexes_by_nt"]]

quintuplet_plots[["normal"]][["insert_sequencer_by_nt"]]

3.1.4 Insertions by RT index, post normalization

3.1.4.1 Rewriting the matrices as cpm to account for library sizes.

knitr::kable(triplets[["normalized"]][["insert_indexes_by_nt"]])

	s2	s3
A	192308	501312
C	176923	91864
G	238462	116798
T	392308	290026

knitr::kable(triplets[["normalized"]][["insert_sequencer_by_nt"]])

	s2	s3
A	75000	156863
C	575000	470588
G	350000	313725
T	0	58824

knitr::kable(quintuplets[["normalized"]][["insert_indexes_by_nt"]])

	s2	s3
A	208333	506631
C	166667	87533
G	225000	118037
T	400000	287798

knitr::kable(quintuplets[["normalized"]][["insert_sequencer_by_nt"]])

	s2	s3
A	0	208333
C	615385	583333
G	384615	208333

3.1.4.2 Rewriting the matrices by dividing by all indexes

I think that there are few enough insertion events that this gets a bit messed up. I will double check the logic of this, but that is my initial guess given how few insertions I was seeing when reading the outputs manually. Unfortunately, this means that for these I also cannot provide a cpm measurement.

knitr::kable(triplets[["matrices_by_counts"]][["insert_indexes_by_nt"]])

	s2	s3
A	0e+00	8e-04
C	0e+00	1e-04
G	0e+00	1e-04
T	1e-04	5e-04

knitr::kable(triplets[["matrices_by_counts"]][["insert_sequencer_by_nt"]])

	s1	s2	s3
A	0	0	0
C	0	0	0
G	0	0	0
T	0	0	0

knitr::kable(quintuplets[["matrices_by_counts"]][["insert_indexes_by_nt"]])

	s2	s3
A	0e+00	8e-04
C	0e+00	1e-04
G	0e+00	1e-04
T	1e-04	5e-04

knitr::kable(quintuplets[["matrices_by_counts"]][["insert_sequencer_by_nt"]])

	s1	s2	s3
A	0	0	0
C	0	0	0
G	0	0	0

The following is my previous writing of this worksheet which just dumped the various tables.

4 Print raw tables

for (t in 1:length(triplets[["matrices"]])) {
  table_name <- names(triplets[["matrices"]])[t]
  message("Raw table: ", table_name, ".")
  print(knitr::kable(triplets[["matrices"]][t]))
}

## Raw table: miss_reads_by_position.

	s1	s2	s3
24	1082	6993	20760
25	1036	9849	12032
26	1450	16847	27910
27	449	4307	11001
28	540	6625	15943
29	1804	12471	17777
30	1454	7791	15889
31	91	1084	3718
32	130	598	1303
33	106	1089	5068
34	816	5685	18000
35	565	8596	25268
36	317	7577	18712
37	1137	6188	20871
38	1016	7734	20169
39	1240	14414	20347
40	375	3848	8694
41	867	4139	14017
42	1144	11326	13853
43	480	5381	10897
44	2066	10012	14480
45	534	6425	30319
46	471	12884	43257
47	838	7950	15358
48	1159	10205	17430
49	1561	15307	18633
50	924	12269	49995
51	597	10377	29519
52	65	6823	30202
53	115	8539	31644
54	2738	14398	28786
55	960	12290	24194
56	1486	6965	13036
57	2984	10992	13140
58	741	6337	10548
59	2875	13858	15395
60	3568	14729	15906
61	1305	9845	25326
62	1222	12216	13584
63	144	5728	11834
64	109	2524	4563
65	606	9498	29124
66	349	12052	46003
67	565	7549	13292
68	1645	7950	12268
69	193	2741	5180
70	199	3866	15935
71	506	7080	21765
72	54	395	2643
73	28	1312	2169
74	67	4837	12258
75	27	5786	22711
76	95	3785	6859
77	1187	7259	16358
78	2548	10363	14476
79	1153	7678	19627
80	700	4522	11538
81	72	842	3529
82	29	2135	4404
83	1890	8222	10287
84	1456	7466	24739
85	95	2096	7659
86	1963	10307	14331
87	1524	10530	29836
88	116	3203	7604
89	359	10556	24941
90	84	2818	13183
91	97	3913	5696
92	807	5349	10673
93	929	8464	16539
94	1509	10402	12369
95	1727	7188	9546
96	1409	8441	10633
97	81	2289	3302
98	64	1508	3568
99	66	820	996
100	1183	24788	35191
101	1375	8722	9267
102	1506	5108	12557
103	720	4350	6665
104	64	2005	5620
105	1906	9748	14336
106	1023	9900	22544
107	86	3649	4915
108	1115	7517	7824
109	1429	8310	11562
110	1879	9961	26921
111	2377	11193	10515
112	678	5301	10315
113	29	4049	15685
114	77	7376	30725
115	268	6009	11200
116	397	4652	15759
117	1251	9629	10311
118	1355	10146	24116
119	1144	9764	9008
120	90	3554	12334
121	157	7343	27886
122	318	5169	9742
123	143	5703	24255
124	744	6867	9647
125	2644	10318	11881
126	3097	11315	26036
127	1443	5851	9749
128	2041	10435	14825
129	2641	13580	14296
130	1354	12595	26333
131	546	5664	14987
132	751	7866	24809
133	1505	5746	12369
134	777	8649	6760
135	209	3516	11733
136	155	2108	5701
137	702	5897	11253
138	1776	7889	10150
139	855	8461	22531
140	641	4670	12971
141	1047	5860	10962
142	439	3068	6764
143	447	4741	9264
144	711	6078	14508
145	816	6578	10844
146	1562	6972	13615
147	69	1314	5387
148	117	3248	11606
149	695	8666	22301
150	154	3349	8572
151	1185	8855	9599
152	196	3986	8473
153	442	3872	8498
154	1090	7333	7978
155	1242	9895	20357
156	1701	10175	12956
157	1222	9816	25575
158	326	4632	11250
159	1326	7498	11609
160	948	7898	26104
161	848	4485	11133
162	853	4855	6857
163	992	9439	9100
164	62	2948	13002
165	55	5558	28535
166	354	5419	9080
167	1339	7420	9698
168	1500	9558	11342
169	1254	9134	19071
170	767	8798	10041
171	170	4624	13537
172	89	8446	36341
173	143	5078	7600
174	946	8412	10086
175	1482	11725	12442
176	2206	10204	21791
177	1713	11666	8792
178	895	8706	20714
179	177	1848	3268
180	75	788	4030
181	70	1310	7292
182	106	1075	2953
183	100	745	2781
184	50	902	4701
185	151	916	4652
186	96	964	6214
187	149	1225	3582
188	130	997	5698
189	117	1216	2763
190	80	1056	3028
191	108	969	3110
192	172	1284	3139
193	34	1177	2858
194	52	800	1806
195	183	2352	4592
196	62	1399	8101
197	77	618	1483
198	229	1426	5243
199	123	1647	4247

## Raw table: miss_indexes_by_position.

	s1	s2	s3
24	197	864	2071
25	219	1108	1298
26	309	1941	2931
27	107	589	1280
28	116	784	1747
29	336	1488	1871
30	311	969	1847
31	23	112	347
32	27	71	179
33	29	124	509
34	191	798	1993
35	128	1002	2706
36	69	969	2266
37	223	778	2286
38	170	887	2110
39	269	1693	2253
40	88	548	1038
41	178	505	1472
42	249	1293	1543
43	105	712	1351
44	345	1107	1549
45	121	784	3079
46	85	1405	4210
47	174	1038	1848
48	238	1209	1694
49	284	1667	1860
50	192	1469	5123
51	127	1263	3078
52	16	721	2996
53	24	917	3188
54	507	1523	2932
55	193	1502	2893
56	268	737	1314
57	598	1210	1359
58	165	965	1410
59	522	1465	1673
60	704	1542	1705
61	254	1133	2701
62	249	1335	1428
63	35	822	1563
64	23	293	498
65	143	1080	3086
66	72	1417	4693
67	118	832	1352
68	298	784	1226
69	32	322	566
70	36	481	1691
71	104	802	2307
72	14	58	280
73	5	134	234
74	14	470	1314
75	0	657	2271
76	19	410	724
77	213	816	1745
78	475	1130	1452
79	239	804	1914
80	131	503	1118
81	16	112	402
82	4	233	488
83	374	937	1121
84	234	835	2486
85	25	269	780
86	374	1190	1392
87	271	1179	2992
88	27	335	824
89	75	1210	2502
90	17	340	1434
91	16	409	621
92	163	588	1082
93	188	936	1598
94	297	1091	1243
95	308	859	1008
96	278	923	1201
97	14	241	356
98	16	197	379
99	12	98	143
100	233	2707	3684
101	289	999	1076
102	286	603	1396
103	149	532	766
104	17	222	571
105	364	1026	1422
106	191	1023	2388
107	20	387	546
108	225	839	812
109	272	906	1210
110	361	1192	2837
111	453	1207	1110
112	138	664	1243
113	7	495	1669
114	15	847	3191
115	63	728	1265
116	82	535	1634
117	253	1070	1106
118	263	1163	2484
119	230	1100	933
120	20	441	1299
121	29	835	2866
122	45	571	1008
123	32	608	2443
124	163	832	1038
125	512	1189	1280
126	535	1301	2682
127	285	661	1058
128	381	1160	1500
129	535	1397	1497
130	264	1406	2639
131	111	712	1726
132	142	804	2538
133	255	676	1291
134	142	1025	736
135	44	399	1246
136	35	264	672
137	131	661	1149
138	342	935	1128
139	157	916	2411
140	124	551	1302
141	202	655	1097
142	85	402	838
143	92	625	1147
144	156	682	1493
145	150	692	1153
146	264	779	1488
147	14	166	558
148	29	372	1232
149	132	1004	2281
150	29	348	978
151	237	1001	975
152	38	492	884
153	94	513	1059
154	225	814	829
155	271	1122	2149
156	331	1176	1374
157	224	1204	2532
158	60	559	1229
159	270	947	1354
160	199	972	2679
161	161	514	1148
162	163	618	824
163	178	1011	977
164	15	358	1331
165	10	651	2996
166	84	723	1093
167	278	898	1096
168	315	1098	1279
169	253	1019	2116
170	158	1044	1071
171	37	535	1521
172	17	966	3784
173	29	603	832
174	149	915	1052
175	310	1384	1314
176	402	1251	2439
177	328	1269	987
178	179	978	2253
179	37	255	435
180	14	119	433
181	11	158	806
182	18	147	348
183	16	115	343
184	11	117	557
185	30	135	548
186	21	125	662
187	29	163	430
188	23	130	634
189	21	170	371
190	17	137	358
191	21	135	379
192	35	195	425
193	6	145	352
194	7	117	235
195	37	293	563
196	12	169	843
197	12	79	197
198	48	216	662
199	27	178	473

## Raw table: miss_sequencer_by_position.

	s1	s2	s3
24	14	185	159
25	46	345	268
26	77	1027	977
27	218	2111	1843
28	31	490	349
29	63	526	424
30	46	2458	2086
31	8	155	115
32	9	114	108
33	35	244	195
34	281	1586	1340
35	73	769	640
36	131	3363	3047
37	292	1753	1518
38	26	776	617
39	165	2380	2126
40	276	2553	2079
41	22	354	250
42	46	1168	1017
43	299	2995	2501
44	51	760	649
45	420	2270	1834
46	29	478	395
47	313	3255	2816
48	61	576	485
49	29	515	407
50	96	492	447
51	64	1174	974
52	37	347	267
53	67	385	318
54	194	1292	1014
55	27	2679	2133
56	25	140	122
57	43	198	163
58	114	1937	1661
59	59	1326	1118
60	360	1510	1323
61	35	294	270
62	72	840	708
63	48	3055	2400
64	46	294	241
65	358	2214	1891
66	34	703	532
67	20	250	203
68	86	472	386
69	30	195	160
70	52	477	375
71	13	120	114
72	19	159	127
73	14	154	133
74	22	278	220
75	18	173	127
76	30	287	257
77	14	110	88
78	27	258	210
79	10	124	115
80	14	103	87
81	17	250	192
82	17	198	170
83	27	259	197
84	16	218	191
85	25	267	212
86	20	225	188
87	22	134	96
88	46	456	394
89	8	115	103
90	26	333	277
91	38	278	250
92	13	89	82
93	3	161	127
94	8	93	67
95	8	71	78
96	18	175	130
97	10	163	143
98	20	216	190
99	25	186	168
100	13	95	80
101	42	331	273
102	29	266	219
103	11	123	109
104	17	172	153
105	10	130	132
106	6	121	118
107	32	245	238
108	7	144	146
109	29	204	180
110	132	692	517
111	28	248	215
112	311	2710	2167
113	16	212	165
114	16	208	177
115	197	1803	1425
116	65	587	500
117	15	158	131
118	77	806	553
119	25	166	134
120	47	511	400
121	50	556	416
122	14	161	124
123	39	477	349
124	69	605	537
125	115	851	639
126	159	1686	836
127	55	671	487
128	119	901	711
129	20	374	319
130	116	1146	949
131	309	2801	2076
132	53	526	465
133	31	318	241
134	30	228	203
135	63	674	565
136	106	798	658
137	46	442	325
138	35	358	297
139	84	734	590
140	94	862	753
141	40	436	337
142	202	1774	1343
143	319	2883	2211
144	31	438	339
145	74	667	552
146	87	920	666
147	22	274	205
148	41	544	394
149	39	342	274
150	53	610	433
151	26	216	179
152	77	687	535
153	257	2320	1859
154	20	206	166
155	90	799	602
156	27	270	218
157	53	598	486
158	103	1143	851
159	75	606	400
160	54	613	470
161	50	592	420
162	118	1226	933
163	38	356	253
164	21	265	207
165	32	322	259
166	192	1959	1403
167	20	240	213
168	35	459	385
169	64	721	555
170	20	244	156
171	69	700	577
172	17	264	195
173	92	803	652
174	11	191	156
175	61	555	467
176	148	1521	1112
177	17	237	191
178	96	989	674
179	49	691	556
180	43	258	222
181	27	233	201
182	49	524	338
183	27	250	233
184	24	271	220
185	30	330	236
186	24	280	235
187	56	522	420
188	33	321	238
189	58	446	361
190	26	289	204
191	43	396	305
192	73	563	481
193	8	187	134
194	18	145	103
195	38	375	279
196	68	522	464
197	31	222	166
198	61	643	505
199	39	418	306

## Raw table: miss_reads_by_string.

	s1	s2	s3
024_mis_C_A	844	4619	6375
024_mis_C_G	0	789	2644
024_mis_C_T	238	1585	11741
025_mis_C_A	795	5897	6746
025_mis_C_G	36	767	1059
025_mis_C_T	205	3185	4227
026_mis_G_A	194	12577	21407
026_mis_G_C	72	1131	2304
026_mis_G_T	1184	3139	4199
027_mis_T_A	4	640	3405
027_mis_T_C	406	1764	4007
027_mis_T_G	39	1903	3589
028_mis_C_A	368	4659	4861
028_mis_C_G	14	242	874
028_mis_C_T	158	1724	10208
029_mis_G_A	133	10108	13500
029_mis_G_C	114	461	815
029_mis_G_T	1557	1902	3462
030_mis_T_A	11	52	569
030_mis_T_C	172	1569	4129
030_mis_T_G	1271	6170	11191
031_mis_T_A	4	509	1691
031_mis_T_C	33	469	1749
031_mis_T_G	54	106	278
032_mis_T_A	4	117	178
032_mis_T_C	107	412	1031
032_mis_T_G	19	69	94
033_mis_T_A	37	194	3092
033_mis_T_C	69	845	1692
033_mis_T_G	0	50	284
034_mis_A_C	319	1081	2062
034_mis_A_G	278	2890	12816
034_mis_A_T	219	1714	3122
035_mis_C_A	443	3561	4583
035_mis_C_G	0	0	626
035_mis_C_T	122	5035	20059
036_mis_A_C	196	4319	11284
036_mis_A_G	118	2900	6310
036_mis_A_T	3	358	1118
037_mis_A_C	639	2828	4752
037_mis_A_G	493	2984	15411
037_mis_A_T	5	376	708
038_mis_C_A	823	4629	7498
038_mis_C_G	31	162	975
038_mis_C_T	162	2943	11696
039_mis_G_A	241	9084	10211
039_mis_G_C	65	2696	5300
039_mis_G_T	934	2634	4836
040_mis_T_A	14	115	1347
040_mis_T_C	335	1593	3666
040_mis_T_G	26	2140	3681
041_mis_C_A	810	3052	7108
041_mis_C_G	18	104	1735
041_mis_C_T	39	983	5174
042_mis_G_A	263	8187	9118
042_mis_G_C	49	975	2797
042_mis_G_T	832	2164	1938
043_mis_T_A	19	676	2221
043_mis_T_C	53	1113	1744
043_mis_T_G	408	3592	6932
044_mis_G_A	78	5635	9360
044_mis_G_C	7	134	500
044_mis_G_T	1981	4243	4620
045_mis_A_C	489	2197	4826
045_mis_A_G	23	3600	24799
045_mis_A_T	22	628	694
046_mis_C_A	352	4982	4858
046_mis_C_G	8	1167	4391
046_mis_C_T	111	6735	34008
047_mis_T_A	66	2770	4201
047_mis_T_C	209	3804	8457
047_mis_T_G	563	1376	2700
048_mis_G_A	103	7512	14055
048_mis_G_C	0	40	65
048_mis_G_T	1056	2653	3310
049_mis_G_A	178	12468	13996
049_mis_G_C	78	385	436
049_mis_G_T	1305	2454	4201
050_mis_G_A	386	11336	48139
050_mis_G_C	47	306	318
050_mis_G_T	491	627	1538
051_mis_A_C	50	428	905
051_mis_A_G	526	9737	28312
051_mis_A_T	21	212	302
052_mis_A_C	45	287	1440
052_mis_A_G	20	6200	28247
052_mis_A_T	0	336	515
053_mis_A_C	86	586	2171
053_mis_A_G	18	7904	28356
053_mis_A_T	11	49	1117
054_mis_A_C	2723	7491	5829
054_mis_A_G	15	6895	22058
054_mis_A_T	0	12	899
055_mis_C_A	818	9541	12336
055_mis_C_G	0	881	974
055_mis_C_T	142	1868	10884
056_mis_C_A	1342	4453	7023
056_mis_C_G	105	347	986
056_mis_C_T	39	2165	5027
057_mis_C_A	1305	6854	7432
057_mis_C_G	0	256	1248
057_mis_C_T	1679	3882	4460
058_mis_T_A	19	1796	3215
058_mis_T_C	614	4085	6370
058_mis_T_G	108	456	963
059_mis_G_A	1200	9572	9206
059_mis_G_C	24	242	409
059_mis_G_T	1651	4044	5780
060_mis_G_A	15	7792	6143
060_mis_G_C	283	1374	2400
060_mis_G_T	3270	5563	7363
061_mis_C_A	1213	5880	5449
061_mis_C_G	54	973	3438
061_mis_C_T	38	2992	16439
062_mis_G_A	184	9013	8638
062_mis_G_C	7	732	1623
062_mis_G_T	1031	2471	3323
063_mis_T_A	3	435	1663
063_mis_T_C	33	666	2013
063_mis_T_G	108	4627	8158
064_mis_T_A	32	1424	1925
064_mis_T_C	71	1072	2347
064_mis_T_G	6	28	291
065_mis_A_C	452	1550	3671
065_mis_A_G	19	5397	19063
065_mis_A_T	135	2551	6390
066_mis_C_A	108	3177	4744
066_mis_C_G	0	717	2784
066_mis_C_T	241	8158	38475
067_mis_C_A	354	4335	5477
067_mis_C_G	0	347	508
067_mis_C_T	211	2867	7307
068_mis_C_A	1462	5875	7246
068_mis_C_G	0	469	1233
068_mis_C_T	183	1606	3789
069_mis_A_C	69	752	838
069_mis_A_G	124	1002	2561
069_mis_A_T	0	987	1781
070_mis_A_C	122	265	1055
070_mis_A_G	61	3315	14411
070_mis_A_T	16	286	469
071_mis_C_A	324	2347	3979
071_mis_C_G	0	826	1716
071_mis_C_T	182	3907	16070
072_mis_T_A	0	176	862
072_mis_T_C	28	170	1644
072_mis_T_G	26	49	137
073_mis_T_A	10	837	746
073_mis_T_C	18	399	1082
073_mis_T_G	0	76	341
074_mis_A_C	20	1065	741
074_mis_A_G	16	3322	9924
074_mis_A_T	31	450	1593
075_mis_A_C	18	451	1855
075_mis_A_G	6	4766	20197
075_mis_A_T	3	569	659
076_mis_T_A	58	2701	3229
076_mis_T_C	37	1005	3337
076_mis_T_G	0	79	293
077_mis_C_A	988	5817	8314
077_mis_C_G	6	316	857
077_mis_C_T	193	1126	7187
078_mis_G_A	72	6326	7553
078_mis_G_C	14	80	331
078_mis_G_T	2462	3957	6592
079_mis_C_A	1107	3922	3782
079_mis_C_G	0	471	2223
079_mis_C_T	46	3285	13622
080_mis_C_A	594	2402	3981
080_mis_C_G	14	34	312
080_mis_C_T	92	2086	7245
081_mis_T_A	27	388	1513
081_mis_T_C	45	327	1434
081_mis_T_G	0	127	582
082_mis_T_A	7	1242	2738
082_mis_T_C	14	789	1508
082_mis_T_G	8	104	158
083_mis_G_A	71	5568	5738
083_mis_G_C	32	99	171
083_mis_G_T	1787	2555	4378
084_mis_C_A	1291	2971	3858
084_mis_C_G	15	158	1142
084_mis_C_T	150	4337	19739
085_mis_A_C	0	169	1068
085_mis_A_G	95	1151	5445
085_mis_A_T	0	776	1146
086_mis_G_A	745	8161	10269
086_mis_G_C	45	150	499
086_mis_G_T	1173	1996	3563
087_mis_C_A	1450	6967	7805
087_mis_C_G	9	1610	3647
087_mis_C_T	65	1953	18384
088_mis_A_C	43	433	913
088_mis_A_G	40	2229	5477
088_mis_A_T	33	541	1214
089_mis_C_A	210	4129	6751
089_mis_C_G	0	947	1948
089_mis_C_T	149	5480	16242
090_mis_A_C	29	665	2005
090_mis_A_G	37	1962	9306
090_mis_A_T	18	191	1872
091_mis_T_A	15	3163	2945
091_mis_T_C	75	701	2596
091_mis_T_G	7	49	155
092_mis_C_A	655	3178	3470
092_mis_C_G	0	476	779
092_mis_C_T	152	1695	6424
093_mis_C_A	794	5827	10902
093_mis_C_G	25	1018	1073
093_mis_C_T	110	1619	4564
094_mis_C_A	1430	9140	6176
094_mis_C_G	9	200	916
094_mis_C_T	70	1062	5277
095_mis_C_A	1664	6189	6731
095_mis_C_G	0	297	775
095_mis_C_T	63	702	2040
096_mis_C_A	1270	6443	4804
096_mis_C_G	0	97	202
096_mis_C_T	139	1901	5627
097_mis_T_A	9	1051	2743
097_mis_T_C	72	928	334
097_mis_T_G	0	310	225
098_mis_T_A	20	1017	2080
098_mis_T_C	21	449	1352
098_mis_T_G	23	42	136
099_mis_T_A	3	117	261
099_mis_T_C	55	674	675
099_mis_T_G	8	29	60
100_mis_C_A	919	3809	3851
100_mis_C_G	13	22	99
100_mis_C_T	251	20957	31241
101_mis_G_A	168	5705	6245
101_mis_G_C	60	173	342
101_mis_G_T	1147	2844	2680
102_mis_C_A	1241	3005	2941
102_mis_C_G	13	130	131
102_mis_C_T	252	1973	9485
103_mis_C_A	567	2995	3048
103_mis_C_G	0	94	303
103_mis_C_T	153	1261	3314
104_mis_A_C	15	508	468
104_mis_A_G	34	885	3333
104_mis_A_T	15	612	1819
105_mis_G_A	65	5986	7998
105_mis_G_C	16	17	47
105_mis_G_T	1825	3745	6291
106_mis_C_A	809	6763	7193
106_mis_C_G	0	810	2377
106_mis_C_T	214	2327	12974
107_mis_T_A	11	2944	3039
107_mis_T_C	40	205	579
107_mis_T_G	35	500	1297
108_mis_G_A	77	5423	5184
108_mis_G_C	28	188	64
108_mis_G_T	1010	1906	2576
109_mis_G_A	67	4494	7114
109_mis_G_C	9	183	92
109_mis_G_T	1353	3633	4356
110_mis_C_A	1239	5200	5680
110_mis_C_G	204	977	1644
110_mis_C_T	436	3784	19597
111_mis_G_A	856	8486	7029
111_mis_G_C	8	187	222
111_mis_G_T	1513	2520	3264
112_mis_T_A	28	1169	2185
112_mis_T_C	247	1224	2135
112_mis_T_G	403	2908	5995
113_mis_A_C	0	110	1049
113_mis_A_G	26	3173	12954
113_mis_A_T	3	766	1682
114_mis_A_C	15	819	2264
114_mis_A_G	24	5885	26420
114_mis_A_T	38	672	2041
115_mis_T_A	89	3898	4177
115_mis_T_C	21	638	4186
115_mis_T_G	158	1473	2837
116_mis_A_C	71	811	1636
116_mis_A_G	279	3716	12085
116_mis_A_T	47	125	2038
117_mis_G_A	16	5299	6530
117_mis_G_C	26	199	299
117_mis_G_T	1209	4131	3482
118_mis_C_A	1168	6116	7357
118_mis_C_G	55	1346	3629
118_mis_C_T	132	2684	13130
119_mis_G_A	138	6781	6286
119_mis_G_C	6	345	227
119_mis_G_T	1000	2638	2495
120_mis_A_C	47	259	920
120_mis_A_G	32	3106	11174
120_mis_A_T	11	189	240
121_mis_A_C	91	669	1986
121_mis_A_G	66	6557	25083
121_mis_A_T	0	117	817
122_mis_G_A	236	4995	8681
122_mis_G_C	5	63	97
122_mis_G_T	77	111	964
123_mis_A_C	36	75	715
123_mis_A_G	104	5533	23422
123_mis_A_T	3	95	118
124_mis_G_A	37	5091	6678
124_mis_G_C	0	38	58
124_mis_G_T	707	1738	2911
125_mis_G_A	165	6239	5568
125_mis_G_C	9	105	154
125_mis_G_T	2470	3974	6159
126_mis_C_A	2554	5323	6184
126_mis_C_G	80	2861	6309
126_mis_C_T	463	3131	13543
127_mis_C_A	1069	4244	5497
127_mis_C_G	52	724	1111
127_mis_C_T	322	883	3141
128_mis_C_A	1534	8168	8694
128_mis_C_G	155	933	2217
128_mis_C_T	352	1334	3914
129_mis_G_A	1076	10259	9520
129_mis_G_C	35	216	304
129_mis_G_T	1530	3105	4472
130_mis_C_A	1246	8553	10968
130_mis_C_G	77	898	3807
130_mis_C_T	31	3144	11558
131_mis_A_C	294	2773	5868
131_mis_A_G	181	2600	7639
131_mis_A_T	71	291	1480
132_mis_C_A	602	2070	4854
132_mis_C_G	8	836	3178
132_mis_C_T	141	4960	16777
133_mis_C_A	1285	4016	5885
133_mis_C_G	34	213	1080
133_mis_C_T	186	1517	5404
134_mis_G_A	232	7298	5459
134_mis_G_C	17	90	249
134_mis_G_T	528	1261	1052
135_mis_A_C	98	448	1605
135_mis_A_G	92	2425	9670
135_mis_A_T	19	643	458
136_mis_T_A	20	844	2718
136_mis_T_C	66	767	2075
136_mis_T_G	69	497	908
137_mis_C_A	562	4267	4514
137_mis_C_G	52	403	1100
137_mis_C_T	88	1227	5639
138_mis_G_A	175	4178	5999
138_mis_G_C	23	285	628
138_mis_G_T	1578	3426	3523
139_mis_C_A	747	3735	4815
139_mis_C_G	36	768	2654
139_mis_C_T	72	3958	15062
140_mis_C_A	429	2557	6306
140_mis_C_G	113	680	1676
140_mis_C_T	99	1433	4989
141_mis_C_A	918	3981	5040
141_mis_C_G	26	451	338
141_mis_C_T	103	1428	5584
142_mis_T_A	73	284	1836
142_mis_T_C	72	976	1778
142_mis_T_G	294	1808	3150
143_mis_T_A	51	1481	2330
143_mis_T_C	58	372	1234
143_mis_T_G	338	2888	5700
144_mis_C_A	596	4314	4740
144_mis_C_G	31	381	1224
144_mis_C_T	84	1383	8544
145_mis_C_A	761	4723	4399
145_mis_C_G	42	251	653
145_mis_C_T	13	1604	5792
146_mis_C_A	1464	6217	9756
146_mis_C_G	3	63	584
146_mis_C_T	95	692	3275
147_mis_A_C	27	134	365
147_mis_A_G	42	1050	3422
147_mis_A_T	0	130	1600
148_mis_A_C	38	348	710
148_mis_A_G	52	2648	10363
148_mis_A_T	27	252	533
149_mis_C_A	482	4273	6331
149_mis_C_G	36	146	459
149_mis_C_T	177	4247	15511
150_mis_A_C	74	425	1815
150_mis_A_G	55	2361	5818
150_mis_A_T	25	563	939
151_mis_G_A	47	6380	6400
151_mis_G_C	3	59	47
151_mis_G_T	1135	2416	3152
152_mis_T_A	31	2650	4114
152_mis_T_C	60	598	1935
152_mis_T_G	105	738	2424
153_mis_T_A	9	1130	2255
153_mis_T_C	131	398	1300
153_mis_T_G	302	2344	4943
154_mis_G_A	95	5380	5849
154_mis_G_C	8	59	179
154_mis_G_T	987	1894	1950
155_mis_C_A	829	4512	6460
155_mis_C_G	55	1300	3262
155_mis_C_T	358	4083	10635
156_mis_G_A	396	7963	8220
156_mis_G_C	9	170	325
156_mis_G_T	1296	2042	4411
157_mis_C_A	1113	7182	7622
157_mis_C_G	24	1219	4389
157_mis_C_T	85	1415	13564
158_mis_A_C	57	527	1690
158_mis_A_G	196	3159	7502
158_mis_A_T	73	946	2058
159_mis_G_A	25	5100	6049
159_mis_G_C	4	80	190
159_mis_G_T	1297	2318	5370
160_mis_C_A	753	4315	7025
160_mis_C_G	68	794	3336
160_mis_C_T	127	2789	15743
161_mis_C_A	775	2659	5423
161_mis_C_G	12	85	502
161_mis_C_T	61	1741	5208
162_mis_T_A	85	2047	2851
162_mis_T_C	494	1461	1790
162_mis_T_G	274	1347	2216
163_mis_G_A	77	6319	6139
163_mis_G_C	0	95	268
163_mis_G_T	915	3025	2693
164_mis_A_C	0	146	1085
164_mis_A_G	30	2636	11265
164_mis_A_T	32	166	652
165_mis_A_C	11	336	1073
165_mis_A_G	40	4842	27010
165_mis_A_T	4	380	452
166_mis_T_A	59	2752	3077
166_mis_T_C	45	743	2060
166_mis_T_G	250	1924	3943
167_mis_G_A	162	5258	7241
167_mis_G_C	0	72	215
167_mis_G_T	1177	2090	2242
168_mis_G_A	175	6834	7903
168_mis_G_C	9	36	272
168_mis_G_T	1316	2688	3167
169_mis_C_A	961	5691	5406
169_mis_C_G	62	749	1331
169_mis_C_T	231	2694	12334
170_mis_G_A	101	6942	7644
170_mis_G_C	79	54	214
170_mis_G_T	587	1802	2183
171_mis_A_C	112	776	1661
171_mis_A_G	33	3562	11283
171_mis_A_T	25	286	593
172_mis_A_C	11	325	3007
172_mis_A_G	54	7837	32160
172_mis_A_T	24	284	1174
173_mis_T_A	56	3267	2393
173_mis_T_C	3	1050	3271
173_mis_T_G	84	761	1936
174_mis_G_A	51	6664	7746
174_mis_G_C	0	73	217
174_mis_G_T	895	1675	2123
175_mis_G_A	139	6873	8064
175_mis_G_C	20	61	70
175_mis_G_T	1323	4791	4308
176_mis_C_A	1486	6364	7314
176_mis_C_G	84	974	3675
176_mis_C_T	636	2866	10802
177_mis_G_A	206	7911	5698
177_mis_G_C	15	410	84
177_mis_G_T	1492	3345	3010
178_mis_C_A	846	3628	5333
178_mis_C_G	26	323	1647
178_mis_C_T	23	4755	13734
179_mis_T_A	46	329	962
179_mis_T_C	30	453	554
179_mis_T_G	101	1066	1752
180_mis_A_C	29	225	1191
180_mis_A_G	28	418	2154
180_mis_A_T	18	145	685
181_mis_A_C	55	389	802
181_mis_A_G	7	764	5882
181_mis_A_T	8	157	608
182_mis_T_A	38	291	770
182_mis_T_C	8	344	1296
182_mis_T_G	60	440	887
183_mis_A_C	57	246	938
183_mis_A_G	33	429	1513
183_mis_A_T	10	70	330
184_mis_A_C	15	459	1125
184_mis_A_G	16	322	3329
184_mis_A_T	19	121	247
185_mis_G_A	53	431	3138
185_mis_G_C	19	97	94
185_mis_G_T	79	388	1420
186_mis_A_C	35	200	937
186_mis_A_G	33	578	4578
186_mis_A_T	28	186	699
187_mis_T_A	36	462	1210
187_mis_T_C	25	281	1396
187_mis_T_G	88	482	976
188_mis_A_C	73	369	946
188_mis_A_G	26	495	4088
188_mis_A_T	31	133	664
189_mis_T_A	37	360	1256
189_mis_T_C	20	255	650
189_mis_T_G	60	601	857
190_mis_C_A	52	911	2005
190_mis_C_G	0	49	200
190_mis_C_T	28	96	823
191_mis_A_C	39	458	937
191_mis_A_G	52	228	1698
191_mis_A_T	17	283	475
192_mis_T_A	23	279	817
192_mis_T_C	33	452	935
192_mis_T_G	116	553	1387
193_mis_C_A	30	713	1020
193_mis_C_G	4	110	177
193_mis_C_T	0	354	1661
194_mis_G_A	21	525	1341
194_mis_G_C	13	88	161
194_mis_G_T	18	187	304
195_mis_G_A	58	1385	2343
195_mis_G_C	31	200	215
195_mis_G_T	94	767	2034
196_mis_C_A	6	429	1413
196_mis_C_G	34	296	1165
196_mis_C_T	22	674	5523
197_mis_T_A	18	75	552
197_mis_T_C	14	144	335
197_mis_T_G	45	399	596
198_mis_T_A	14	197	838
198_mis_T_C	42	222	1412
198_mis_T_G	173	1007	2993
199_mis_T_A	5	637	1415
199_mis_T_C	53	622	1719
199_mis_T_G	65	388	1113

## Raw table: miss_indexes_by_string.

	s1	s2	s3
024_mis_C_A	157	563	620
024_mis_C_G	0	105	292
024_mis_C_T	40	196	1159
025_mis_C_A	166	675	680
025_mis_C_G	8	104	123
025_mis_C_T	45	329	495
026_mis_G_A	40	1415	2165
026_mis_G_C	22	173	352
026_mis_G_T	247	353	414
027_mis_T_A	0	93	321
027_mis_T_C	98	231	463
027_mis_T_G	9	265	496
028_mis_C_A	70	533	548
028_mis_C_G	3	33	105
028_mis_C_T	43	218	1094
029_mis_G_A	22	1180	1363
029_mis_G_C	24	63	106
029_mis_G_T	290	245	402
030_mis_T_A	3	9	65
030_mis_T_C	32	179	381
030_mis_T_G	276	781	1401
031_mis_T_A	0	34	125
031_mis_T_C	9	64	187
031_mis_T_G	14	14	35
032_mis_T_A	0	18	20
032_mis_T_C	22	43	148
032_mis_T_G	5	10	11
033_mis_T_A	10	26	290
033_mis_T_C	19	91	192
033_mis_T_G	0	7	27
034_mis_A_C	66	133	232
034_mis_A_G	62	338	1330
034_mis_A_T	63	327	431
035_mis_C_A	100	427	537
035_mis_C_G	0	0	70
035_mis_C_T	28	575	2099
036_mis_A_C	42	611	1510
036_mis_A_G	27	313	638
036_mis_A_T	0	45	118
037_mis_A_C	125	336	554
037_mis_A_G	98	400	1658
037_mis_A_T	0	42	74
038_mis_C_A	130	515	794
038_mis_C_G	7	22	84
038_mis_C_T	33	350	1232
039_mis_G_A	50	983	1011
039_mis_G_C	21	389	745
039_mis_G_T	198	321	497
040_mis_T_A	3	21	143
040_mis_T_C	79	219	398
040_mis_T_G	6	308	497
041_mis_C_A	165	376	735
041_mis_C_G	4	12	166
041_mis_C_T	9	117	571
042_mis_G_A	45	884	913
042_mis_G_C	11	149	385
042_mis_G_T	193	260	245
043_mis_T_A	4	70	214
043_mis_T_C	11	128	212
043_mis_T_G	90	514	925
044_mis_G_A	18	663	986
044_mis_G_C	0	15	46
044_mis_G_T	327	429	517
045_mis_A_C	108	267	537
045_mis_A_G	7	452	2471
045_mis_A_T	6	65	71
046_mis_C_A	61	567	583
046_mis_C_G	0	133	379
046_mis_C_T	24	705	3248
047_mis_T_A	12	315	399
047_mis_T_C	46	551	1140
047_mis_T_G	116	172	309
048_mis_G_A	24	860	1282
048_mis_G_C	0	8	9
048_mis_G_T	214	341	403
049_mis_G_A	30	1342	1381
049_mis_G_C	16	41	47
049_mis_G_T	238	284	432
050_mis_G_A	73	1341	4895
050_mis_G_C	8	35	39
050_mis_G_T	111	93	189
051_mis_A_C	10	55	107
051_mis_A_G	112	1182	2927
051_mis_A_T	5	26	44
052_mis_A_C	11	46	147
052_mis_A_G	5	646	2794
052_mis_A_T	0	29	55
053_mis_A_C	19	68	239
053_mis_A_G	5	839	2824
053_mis_A_T	0	10	125
054_mis_A_C	503	809	688
054_mis_A_G	4	714	2159
054_mis_A_T	0	0	85
055_mis_C_A	162	1199	1611
055_mis_C_G	0	84	108
055_mis_C_T	31	219	1174
056_mis_C_A	245	502	681
056_mis_C_G	14	33	102
056_mis_C_T	9	202	531
057_mis_C_A	273	747	806
057_mis_C_G	0	25	92
057_mis_C_T	325	438	461
058_mis_T_A	6	211	308
058_mis_T_C	136	695	990
058_mis_T_G	23	59	112
059_mis_G_A	219	954	947
059_mis_G_C	7	40	53
059_mis_G_T	296	471	673
060_mis_G_A	5	772	658
060_mis_G_C	62	175	281
060_mis_G_T	637	595	766
061_mis_C_A	231	658	634
061_mis_C_G	14	139	367
061_mis_C_T	9	336	1700
062_mis_G_A	40	940	845
062_mis_G_C	0	104	213
062_mis_G_T	209	291	370
063_mis_T_A	0	38	156
063_mis_T_C	9	86	235
063_mis_T_G	26	698	1172
064_mis_T_A	8	176	222
064_mis_T_C	15	114	243
064_mis_T_G	0	3	33
065_mis_A_C	103	218	431
065_mis_A_G	4	511	1911
065_mis_A_T	36	351	744
066_mis_C_A	27	398	555
066_mis_C_G	0	72	286
066_mis_C_T	45	947	3852
067_mis_C_A	69	462	552
067_mis_C_G	0	47	54
067_mis_C_T	49	323	746
068_mis_C_A	255	598	749
068_mis_C_G	0	42	119
068_mis_C_T	43	144	358
069_mis_A_C	12	84	94
069_mis_A_G	20	129	299
069_mis_A_T	0	109	173
070_mis_A_C	19	34	127
070_mis_A_G	14	407	1492
070_mis_A_T	3	40	72
071_mis_C_A	76	278	424
071_mis_C_G	0	79	202
071_mis_C_T	28	445	1681
072_mis_T_A	0	19	92
072_mis_T_C	6	31	168
072_mis_T_G	8	8	20
073_mis_T_A	0	80	84
073_mis_T_C	5	44	112
073_mis_T_G	0	10	38
074_mis_A_C	3	96	87
074_mis_A_G	4	323	1050
074_mis_A_T	7	51	177
075_mis_A_C	0	62	184
075_mis_A_G	0	533	2019
075_mis_A_T	0	62	68
076_mis_T_A	12	285	320
076_mis_T_C	7	112	364
076_mis_T_G	0	13	40
077_mis_C_A	174	618	858
077_mis_C_G	0	40	103
077_mis_C_T	39	158	784
078_mis_G_A	17	684	775
078_mis_G_C	4	13	46
078_mis_G_T	454	433	631
079_mis_C_A	227	426	396
079_mis_C_G	0	58	244
079_mis_C_T	12	320	1274
080_mis_C_A	108	271	375
080_mis_C_G	4	4	29
080_mis_C_T	19	228	714
081_mis_T_A	5	55	191
081_mis_T_C	11	40	151
081_mis_T_G	0	17	60
082_mis_T_A	0	132	301
082_mis_T_C	4	88	166
082_mis_T_G	0	13	21
083_mis_G_A	15	620	649
083_mis_G_C	9	16	23
083_mis_G_T	350	301	449
084_mis_C_A	200	304	403
084_mis_C_G	0	27	102
084_mis_C_T	34	504	1981
085_mis_A_C	0	28	102
085_mis_A_G	25	158	576
085_mis_A_T	0	83	102
086_mis_G_A	120	893	975
086_mis_G_C	12	22	59
086_mis_G_T	242	275	358
087_mis_C_A	252	773	826
087_mis_C_G	3	180	385
087_mis_C_T	16	226	1781
088_mis_A_C	9	63	118
088_mis_A_G	11	227	581
088_mis_A_T	7	45	125
089_mis_C_A	43	486	656
089_mis_C_G	0	109	171
089_mis_C_T	32	615	1675
090_mis_A_C	5	81	240
090_mis_A_G	8	233	997
090_mis_A_T	4	26	197
091_mis_T_A	0	312	315
091_mis_T_C	16	90	286
091_mis_T_G	0	7	20
092_mis_C_A	132	335	360
092_mis_C_G	0	59	83
092_mis_C_T	31	194	639
093_mis_C_A	161	654	1074
093_mis_C_G	7	111	118
093_mis_C_T	20	171	406
094_mis_C_A	280	944	631
094_mis_C_G	3	30	115
094_mis_C_T	14	117	497
095_mis_C_A	294	736	673
095_mis_C_G	0	35	97
095_mis_C_T	14	88	238
096_mis_C_A	248	677	558
096_mis_C_G	0	17	40
096_mis_C_T	30	229	603
097_mis_T_A	0	122	286
097_mis_T_C	14	86	44
097_mis_T_G	0	33	26
098_mis_T_A	6	125	220
098_mis_T_C	5	66	139
098_mis_T_G	5	6	20
099_mis_T_A	0	15	33
099_mis_T_C	12	78	98
099_mis_T_G	0	5	12
100_mis_C_A	179	455	428
100_mis_C_G	3	5	11
100_mis_C_T	51	2247	3245
101_mis_G_A	40	642	708
101_mis_G_C	16	24	44
101_mis_G_T	233	333	324
102_mis_C_A	235	334	315
102_mis_C_G	0	12	22
102_mis_C_T	51	257	1059
103_mis_C_A	113	360	309
103_mis_C_G	0	14	38
103_mis_C_T	36	158	419
104_mis_A_C	4	52	51
104_mis_A_G	8	96	350
104_mis_A_T	5	74	170
105_mis_G_A	17	615	829
105_mis_G_C	4	0	6
105_mis_G_T	343	411	587
106_mis_C_A	149	671	738
106_mis_C_G	0	65	241
106_mis_C_T	42	287	1409
107_mis_T_A	0	291	323
107_mis_T_C	11	32	82
107_mis_T_G	9	64	141
108_mis_G_A	15	572	540
108_mis_G_C	6	22	10
108_mis_G_T	204	245	262
109_mis_G_A	13	467	731
109_mis_G_C	0	20	14
109_mis_G_T	259	419	465
110_mis_C_A	223	655	635
110_mis_C_G	41	98	200
110_mis_C_T	97	439	2002
111_mis_G_A	147	878	731
111_mis_G_C	0	19	25
111_mis_G_T	306	310	354
112_mis_T_A	7	137	252
112_mis_T_C	49	116	218
112_mis_T_G	82	411	773
113_mis_A_C	0	17	108
113_mis_A_G	7	403	1384
113_mis_A_T	0	75	177
114_mis_A_C	3	79	270
114_mis_A_G	6	685	2710
114_mis_A_T	6	83	211
115_mis_T_A	20	447	478
115_mis_T_C	6	94	411
115_mis_T_G	37	187	376
116_mis_A_C	17	97	207
116_mis_A_G	57	421	1257
116_mis_A_T	8	17	170
117_mis_G_A	4	626	677
117_mis_G_C	4	25	28
117_mis_G_T	245	419	401
118_mis_C_A	224	691	715
118_mis_C_G	11	161	398
118_mis_C_T	28	311	1371
119_mis_G_A	27	750	636
119_mis_G_C	0	36	31
119_mis_G_T	203	314	266
120_mis_A_C	10	38	118
120_mis_A_G	7	380	1143
120_mis_A_T	3	23	38
121_mis_A_C	14	68	171
121_mis_A_G	15	749	2607
121_mis_A_T	0	18	88
122_mis_G_A	33	544	882
122_mis_G_C	0	9	14
122_mis_G_T	12	18	112
123_mis_A_C	6	10	82
123_mis_A_G	26	582	2340
123_mis_A_T	0	16	21
124_mis_G_A	11	609	678
124_mis_G_C	0	7	10
124_mis_G_T	152	216	350
125_mis_G_A	37	675	589
125_mis_G_C	3	17	21
125_mis_G_T	472	497	670
126_mis_C_A	433	605	677
126_mis_C_G	17	327	669
126_mis_C_T	85	369	1336
127_mis_C_A	213	473	585
127_mis_C_G	12	75	131
127_mis_C_T	60	113	342
128_mis_C_A	295	872	850
128_mis_C_G	28	121	287
128_mis_C_T	58	167	363
129_mis_G_A	215	1024	1010
129_mis_G_C	9	27	42
129_mis_G_T	311	346	445
130_mis_C_A	240	938	1050
130_mis_C_G	15	118	403
130_mis_C_T	9	350	1186
131_mis_A_C	65	377	757
131_mis_A_G	34	301	822
131_mis_A_T	12	34	147
132_mis_C_A	109	228	513
132_mis_C_G	0	102	321
132_mis_C_T	33	474	1704
133_mis_C_A	200	467	589
133_mis_C_G	8	26	136
133_mis_C_T	47	183	566
134_mis_G_A	40	864	584
134_mis_G_C	3	12	33
134_mis_G_T	99	149	119
135_mis_A_C	20	62	181
135_mis_A_G	19	258	1005
135_mis_A_T	5	79	60
136_mis_T_A	4	100	302
136_mis_T_C	16	98	251
136_mis_T_G	15	66	119
137_mis_C_A	101	478	487
137_mis_C_G	11	46	134
137_mis_C_T	19	137	528
138_mis_G_A	36	494	671
138_mis_G_C	5	39	72
138_mis_G_T	301	402	385
139_mis_C_A	134	393	563
139_mis_C_G	7	97	293
139_mis_C_T	16	426	1555
140_mis_C_A	75	294	602
140_mis_C_G	22	70	168
140_mis_C_T	27	187	532
141_mis_C_A	173	433	509
141_mis_C_G	5	41	41
141_mis_C_T	24	181	547
142_mis_T_A	13	43	219
142_mis_T_C	14	116	208
142_mis_T_G	58	243	411
143_mis_T_A	9	180	254
143_mis_T_C	15	54	162
143_mis_T_G	68	391	731
144_mis_C_A	129	467	486
144_mis_C_G	6	41	139
144_mis_C_T	21	174	868
145_mis_C_A	137	488	539
145_mis_C_G	9	37	66
145_mis_C_T	4	167	548
146_mis_C_A	240	688	1100
146_mis_C_G	0	9	51
146_mis_C_T	24	82	337
147_mis_A_C	5	19	49
147_mis_A_G	9	125	368
147_mis_A_T	0	22	141
148_mis_A_C	8	45	90
148_mis_A_G	15	299	1073
148_mis_A_T	6	28	69
149_mis_C_A	102	508	669
149_mis_C_G	7	24	66
149_mis_C_T	23	472	1546
150_mis_A_C	14	55	224
150_mis_A_G	10	239	655
150_mis_A_T	5	54	99
151_mis_G_A	8	733	659
151_mis_G_C	0	8	7
151_mis_G_T	229	260	309
152_mis_T_A	7	303	407
152_mis_T_C	11	85	202
152_mis_T_G	20	104	275
153_mis_T_A	3	132	244
153_mis_T_C	28	49	167
153_mis_T_G	63	332	648
154_mis_G_A	18	590	573
154_mis_G_C	0	8	23
154_mis_G_T	207	216	233
155_mis_C_A	172	499	653
155_mis_C_G	13	155	349
155_mis_C_T	86	468	1147
156_mis_G_A	71	869	897
156_mis_G_C	0	20	45
156_mis_G_T	260	287	432
157_mis_C_A	199	850	799
157_mis_C_G	4	155	457
157_mis_C_T	21	199	1276
158_mis_A_C	11	72	177
158_mis_A_G	36	383	844
158_mis_A_T	13	104	208
159_mis_G_A	7	625	715
159_mis_G_C	0	12	28
159_mis_G_T	263	310	611
160_mis_C_A	153	538	647
160_mis_C_G	12	106	354
160_mis_C_T	34	328	1678
161_mis_C_A	143	322	555
161_mis_C_G	0	13	60
161_mis_C_T	18	179	533
162_mis_T_A	19	242	318
162_mis_T_C	92	192	215
162_mis_T_G	52	184	291
163_mis_G_A	14	691	671
163_mis_G_C	0	11	29
163_mis_G_T	164	309	277
164_mis_A_C	0	17	116
164_mis_A_G	8	322	1129
164_mis_A_T	7	19	86
165_mis_A_C	0	37	131
165_mis_A_G	10	564	2803
165_mis_A_T	0	50	62
166_mis_T_A	14	374	391
166_mis_T_C	13	97	213
166_mis_T_G	57	252	489
167_mis_G_A	37	621	825
167_mis_G_C	0	10	23
167_mis_G_T	241	267	248
168_mis_G_A	49	772	895
168_mis_G_C	3	4	33
168_mis_G_T	263	322	351
169_mis_C_A	192	622	639
169_mis_C_G	14	96	174
169_mis_C_T	47	301	1303
170_mis_G_A	21	825	793
170_mis_G_C	15	7	26
170_mis_G_T	122	212	252
171_mis_A_C	23	103	206
171_mis_A_G	8	400	1242
171_mis_A_T	6	32	73
172_mis_A_C	0	47	280
172_mis_A_G	10	882	3383
172_mis_A_T	7	37	121
173_mis_T_A	13	372	283
173_mis_T_C	0	114	298
173_mis_T_G	16	117	251
174_mis_G_A	11	702	788
174_mis_G_C	0	8	29
174_mis_G_T	138	205	235
175_mis_G_A	31	792	813
175_mis_G_C	4	8	11
175_mis_G_T	275	584	490
176_mis_C_A	250	767	780
176_mis_C_G	18	119	397
176_mis_C_T	134	365	1262
177_mis_G_A	41	853	638
177_mis_G_C	5	37	12
177_mis_G_T	282	379	337
178_mis_C_A	169	414	592
178_mis_C_G	5	54	198
178_mis_C_T	5	510	1463
179_mis_T_A	10	50	121
179_mis_T_C	8	71	86
179_mis_T_G	19	134	228
180_mis_A_C	6	39	122
180_mis_A_G	5	55	241
180_mis_A_T	3	25	70
181_mis_A_C	11	49	107
181_mis_A_G	0	81	622
181_mis_A_T	0	28	77
182_mis_T_A	8	43	94
182_mis_T_C	0	42	134
182_mis_T_G	10	62	120
183_mis_A_C	9	37	108
183_mis_A_G	7	68	195
183_mis_A_T	0	10	40
184_mis_A_C	3	55	126
184_mis_A_G	4	47	390
184_mis_A_T	4	15	41
185_mis_G_A	10	70	364
185_mis_G_C	3	13	13
185_mis_G_T	17	52	171
186_mis_A_C	8	31	104
186_mis_A_G	7	66	484
186_mis_A_T	6	28	74
187_mis_T_A	7	64	160
187_mis_T_C	4	32	138
187_mis_T_G	18	67	132
188_mis_A_C	14	53	113
188_mis_A_G	4	56	436
188_mis_A_T	5	21	85
189_mis_T_A	7	52	164
189_mis_T_C	4	38	92
189_mis_T_G	10	80	115
190_mis_C_A	11	116	224
190_mis_C_G	0	9	27
190_mis_C_T	6	12	107
191_mis_A_C	8	66	123
191_mis_A_G	10	29	192
191_mis_A_T	3	40	64
192_mis_T_A	5	46	114
192_mis_T_C	8	64	127
192_mis_T_G	22	85	184
193_mis_C_A	6	88	136
193_mis_C_G	0	14	22
193_mis_C_T	0	43	194
194_mis_G_A	4	75	164
194_mis_G_C	0	12	24
194_mis_G_T	3	30	47
195_mis_G_A	10	177	319
195_mis_G_C	7	25	30
195_mis_G_T	20	91	214
196_mis_C_A	0	50	148
196_mis_C_G	7	38	149
196_mis_C_T	5	81	546
197_mis_T_A	3	8	61
197_mis_T_C	0	22	52
197_mis_T_G	9	49	84
198_mis_T_A	4	27	97
198_mis_T_C	8	36	162
198_mis_T_G	36	153	403
199_mis_T_A	0	52	145
199_mis_T_C	11	78	186
199_mis_T_G	16	48	142

## Raw table: miss_sequencer_by_string.

	s1	s2	s3
024_mis_C_A	5	50	43
024_mis_C_G	0	52	44
024_mis_C_T	9	83	72
025_mis_C_A	14	77	59
025_mis_C_G	16	131	87
025_mis_C_T	16	137	122
026_mis_G_A	9	142	129
026_mis_G_C	11	551	611
026_mis_G_T	57	334	237
027_mis_T_A	4	75	67
027_mis_T_C	209	876	811
027_mis_T_G	5	1160	965
028_mis_C_A	3	36	57
028_mis_C_G	19	146	100
028_mis_C_T	9	308	192
029_mis_G_A	7	74	66
029_mis_G_C	4	187	156
029_mis_G_T	52	265	202
030_mis_T_A	4	25	18
030_mis_T_C	14	155	123
030_mis_T_G	28	2278	1945
031_mis_T_A	0	20	13
031_mis_T_C	8	99	73
031_mis_T_G	0	36	29
032_mis_T_A	0	19	18
032_mis_T_C	4	70	65
032_mis_T_G	5	25	25
033_mis_T_A	26	107	85
033_mis_T_C	9	120	82
033_mis_T_G	0	17	28
034_mis_A_C	259	1046	909
034_mis_A_G	6	100	77
034_mis_A_T	16	440	354
035_mis_C_A	65	694	556
035_mis_C_G	0	7	14
035_mis_C_T	8	68	70
036_mis_A_C	112	3225	2938
036_mis_A_G	16	114	92
036_mis_A_T	3	24	17
037_mis_A_C	282	1644	1433
037_mis_A_G	10	84	63
037_mis_A_T	0	25	22
038_mis_C_A	4	656	502
038_mis_C_G	10	53	52
038_mis_C_T	12	67	63
039_mis_G_A	18	134	111
039_mis_G_C	13	1574	1477
039_mis_G_T	134	672	538
040_mis_T_A	0	64	51
040_mis_T_C	265	1206	983
040_mis_T_G	11	1283	1045
041_mis_C_A	5	54	42
041_mis_C_G	4	66	54
041_mis_C_T	13	234	154
042_mis_G_A	8	117	87
042_mis_G_C	8	804	709
042_mis_G_T	30	247	221
043_mis_T_A	14	85	99
043_mis_T_C	29	229	175
043_mis_T_G	256	2681	2227
044_mis_G_A	33	225	183
044_mis_G_C	6	38	31
044_mis_G_T	12	497	435
045_mis_A_C	399	1920	1532
045_mis_A_G	13	260	229
045_mis_A_T	8	90	73
046_mis_C_A	4	364	296
046_mis_C_G	0	11	17
046_mis_C_T	25	103	82
047_mis_T_A	3	46	37
047_mis_T_C	36	2279	1925
047_mis_T_G	274	930	854
048_mis_G_A	8	107	74
048_mis_G_C	4	30	22
048_mis_G_T	49	439	389
049_mis_G_A	8	128	95
049_mis_G_C	6	39	27
049_mis_G_T	15	348	285
050_mis_G_A	57	302	272
050_mis_G_C	3	39	20
050_mis_G_T	36	151	155
051_mis_A_C	31	264	231
051_mis_A_G	22	842	691
051_mis_A_T	11	68	52
052_mis_A_C	25	217	177
052_mis_A_G	12	114	80
052_mis_A_T	0	16	10
053_mis_A_C	61	309	264
053_mis_A_G	6	63	46
053_mis_A_T	0	13	8
054_mis_A_C	183	1220	958
054_mis_A_G	5	56	40
054_mis_A_T	6	16	16
055_mis_C_A	21	2623	2098
055_mis_C_G	0	0	5
055_mis_C_T	6	56	30
056_mis_C_A	15	77	61
056_mis_C_G	0	11	5
056_mis_C_T	10	52	56
057_mis_C_A	7	34	43
057_mis_C_G	0	11	5
057_mis_C_T	36	153	115
058_mis_T_A	10	58	58
058_mis_T_C	28	1509	1264
058_mis_T_G	76	370	339
059_mis_G_A	19	120	107
059_mis_G_C	16	103	69
059_mis_G_T	24	1103	942
060_mis_G_A	7	54	54
060_mis_G_C	283	1172	1025
060_mis_G_T	70	284	244
061_mis_C_A	5	29	38
061_mis_C_G	16	138	121
061_mis_C_T	14	127	111
062_mis_G_A	7	71	52
062_mis_G_C	5	503	457
062_mis_G_T	60	266	199
063_mis_T_A	10	78	74
063_mis_T_C	17	239	166
063_mis_T_G	21	2738	2160
064_mis_T_A	32	131	125
064_mis_T_C	11	146	104
064_mis_T_G	3	17	12
065_mis_A_C	327	1462	1227
065_mis_A_G	13	80	66
065_mis_A_T	18	672	598
066_mis_C_A	27	614	459
066_mis_C_G	0	10	12
066_mis_C_T	7	79	61
067_mis_C_A	9	164	124
067_mis_C_G	0	17	15
067_mis_C_T	11	69	64
068_mis_C_A	76	370	306
068_mis_C_G	0	16	15
068_mis_C_T	10	86	65
069_mis_A_C	19	99	80
069_mis_A_G	11	79	69
069_mis_A_T	0	17	11
070_mis_A_C	37	297	228
070_mis_A_G	7	109	81
070_mis_A_T	8	71	66
071_mis_C_A	6	78	68
071_mis_C_G	0	5	6
071_mis_C_T	7	37	40
072_mis_T_A	3	25	20
072_mis_T_C	7	98	70
072_mis_T_G	9	36	37
073_mis_T_A	4	45	38
073_mis_T_C	7	86	67
073_mis_T_G	3	23	28
074_mis_A_C	4	127	92
074_mis_A_G	5	61	63
074_mis_A_T	13	90	65
075_mis_A_C	6	68	38
075_mis_A_G	7	60	44
075_mis_A_T	5	45	45
076_mis_T_A	8	133	111
076_mis_T_C	19	98	95
076_mis_T_G	3	56	51
077_mis_C_A	7	36	22
077_mis_C_G	0	7	11
077_mis_C_T	7	67	55
078_mis_G_A	8	129	89
078_mis_G_C	7	72	61
078_mis_G_T	12	57	60
079_mis_C_A	6	63	67
079_mis_C_G	0	23	13
079_mis_C_T	4	38	35
080_mis_C_A	8	37	29
080_mis_C_G	0	8	7
080_mis_C_T	6	58	51
081_mis_T_A	0	54	51
081_mis_T_C	13	110	88
081_mis_T_G	4	86	53
082_mis_T_A	4	40	23
082_mis_T_C	13	124	116
082_mis_T_G	0	34	31
083_mis_G_A	6	80	61
083_mis_G_C	9	58	38
083_mis_G_T	12	121	98
084_mis_C_A	0	35	27
084_mis_C_G	3	24	28
084_mis_C_T	13	159	136
085_mis_A_C	7	107	55
085_mis_A_G	18	142	142
085_mis_A_T	0	18	15
086_mis_G_A	3	104	87
086_mis_G_C	10	47	47
086_mis_G_T	7	74	54
087_mis_C_A	18	58	44
087_mis_C_G	0	16	7
087_mis_C_T	4	60	45
088_mis_A_C	20	235	196
088_mis_A_G	14	115	116
088_mis_A_T	12	106	82
089_mis_C_A	3	40	39
089_mis_C_G	0	9	8
089_mis_C_T	5	66	56
090_mis_A_C	3	164	142
090_mis_A_G	15	92	82
090_mis_A_T	8	77	53
091_mis_T_A	6	87	73
091_mis_T_C	17	149	132
091_mis_T_G	15	42	45
092_mis_C_A	6	31	26
092_mis_C_G	3	17	6
092_mis_C_T	4	41	50
093_mis_C_A	3	72	58
093_mis_C_G	0	16	18
093_mis_C_T	0	73	51
094_mis_C_A	4	41	26
094_mis_C_G	0	13	13
094_mis_C_T	4	39	28
095_mis_C_A	0	23	36
095_mis_C_G	0	14	7
095_mis_C_T	8	34	35
096_mis_C_A	5	40	27
096_mis_C_G	0	6	5
096_mis_C_T	13	129	98
097_mis_T_A	5	33	34
097_mis_T_C	5	107	98
097_mis_T_G	0	23	11
098_mis_T_A	3	61	46
098_mis_T_C	8	121	105
098_mis_T_G	9	34	39
099_mis_T_A	0	23	15
099_mis_T_C	19	127	120
099_mis_T_G	6	36	33
100_mis_C_A	3	16	12
100_mis_C_G	0	7	0
100_mis_C_T	10	72	68
101_mis_G_A	25	200	178
101_mis_G_C	7	74	59
101_mis_G_T	10	57	36
102_mis_C_A	6	48	42
102_mis_C_G	0	21	24
102_mis_C_T	23	197	153
103_mis_C_A	0	28	18
103_mis_C_G	0	12	19
103_mis_C_T	11	83	72
104_mis_A_C	0	41	46
104_mis_A_G	12	108	81
104_mis_A_T	5	23	26
105_mis_G_A	3	47	37
105_mis_G_C	0	13	15
105_mis_G_T	7	70	80
106_mis_C_A	6	71	72
106_mis_C_G	0	16	13
106_mis_C_T	0	34	33
107_mis_T_A	5	22	27
107_mis_T_C	9	104	79
107_mis_T_G	18	119	132
108_mis_G_A	7	67	74
108_mis_G_C	0	21	21
108_mis_G_T	0	56	51
109_mis_G_A	14	130	107
109_mis_G_C	0	9	17
109_mis_G_T	15	65	56
110_mis_C_A	25	115	77
110_mis_C_G	78	312	225
110_mis_C_T	29	265	215
111_mis_G_A	16	149	114
111_mis_G_C	0	33	26
111_mis_G_T	12	66	75
112_mis_T_A	25	205	162
112_mis_T_C	8	84	61
112_mis_T_G	278	2421	1944
113_mis_A_C	0	16	12
113_mis_A_G	13	157	118
113_mis_A_T	3	39	35
114_mis_A_C	0	21	17
114_mis_A_G	12	109	109
114_mis_A_T	4	78	51
115_mis_T_A	60	561	436
115_mis_T_C	9	103	87
115_mis_T_G	128	1139	902
116_mis_A_C	26	275	268
116_mis_A_G	30	267	201
116_mis_A_T	9	45	31
117_mis_G_A	4	74	58
117_mis_G_C	7	48	39
117_mis_G_T	4	36	34
118_mis_C_A	28	276	178
118_mis_C_G	40	412	273
118_mis_C_T	9	118	102
119_mis_G_A	13	85	66
119_mis_G_C	3	44	44
119_mis_G_T	9	37	24
120_mis_A_C	17	215	141
120_mis_A_G	27	248	206
120_mis_A_T	3	48	53
121_mis_A_C	0	37	37
121_mis_A_G	47	482	357
121_mis_A_T	3	37	22
122_mis_G_A	7	74	65
122_mis_G_C	0	31	21
122_mis_G_T	7	56	38
123_mis_A_C	0	26	17
123_mis_A_G	39	425	315
123_mis_A_T	0	26	17
124_mis_G_A	11	112	79
124_mis_G_C	0	17	17
124_mis_G_T	58	476	441
125_mis_G_A	15	78	72
125_mis_G_C	5	48	37
125_mis_G_T	95	725	530
126_mis_C_A	24	241	101
126_mis_C_G	62	690	378
126_mis_C_T	73	755	357
127_mis_C_A	20	205	145
127_mis_C_G	7	163	125
127_mis_C_T	28	303	217
128_mis_C_A	53	290	242
128_mis_C_G	39	355	271
128_mis_C_T	27	256	198
129_mis_G_A	16	258	227
129_mis_G_C	4	69	56
129_mis_G_T	0	47	36
130_mis_C_A	73	721	629
130_mis_C_G	37	327	243
130_mis_C_T	6	98	77
131_mis_A_C	262	2346	1733
131_mis_A_G	44	390	289
131_mis_A_T	3	65	54
132_mis_C_A	33	345	292
132_mis_C_G	12	122	110
132_mis_C_T	8	59	63
133_mis_C_A	10	120	66
133_mis_C_G	10	136	100
133_mis_C_T	11	62	75
134_mis_G_A	12	77	74
134_mis_G_C	4	38	30
134_mis_G_T	14	113	99
135_mis_A_C	22	323	258
135_mis_A_G	34	266	241
135_mis_A_T	7	85	66
136_mis_T_A	22	182	129
136_mis_T_C	30	270	211
136_mis_T_G	54	346	318
137_mis_C_A	19	191	132
137_mis_C_G	13	143	113
137_mis_C_T	14	108	80
138_mis_G_A	19	169	151
138_mis_G_C	12	128	96
138_mis_G_T	4	61	50
139_mis_C_A	60	499	385
139_mis_C_G	19	164	138
139_mis_C_T	5	71	67
140_mis_C_A	70	517	449
140_mis_C_G	13	244	220
140_mis_C_T	11	101	84
141_mis_C_A	19	174	137
141_mis_C_G	5	72	53
141_mis_C_T	16	190	147
142_mis_T_A	10	78	73
142_mis_T_C	19	205	165
142_mis_T_G	173	1491	1105
143_mis_T_A	23	165	121
143_mis_T_C	32	301	194
143_mis_T_G	264	2417	1896
144_mis_C_A	15	186	169
144_mis_C_G	10	124	76
144_mis_C_T	6	128	94
145_mis_C_A	59	529	429
145_mis_C_G	5	51	47
145_mis_C_T	10	87	76
146_mis_C_A	76	796	561
146_mis_C_G	0	31	23
146_mis_C_T	11	93	82
147_mis_A_C	12	104	58
147_mis_A_G	10	139	114
147_mis_A_T	0	31	33
148_mis_A_C	21	242	163
148_mis_A_G	15	191	148
148_mis_A_T	5	111	83
149_mis_C_A	30	263	202
149_mis_C_G	6	27	20
149_mis_C_T	3	52	52
150_mis_A_C	35	320	235
150_mis_A_G	18	265	177
150_mis_A_T	0	25	21
151_mis_G_A	15	93	85
151_mis_G_C	0	13	10
151_mis_G_T	11	110	84
152_mis_T_A	5	60	43
152_mis_T_C	10	92	108
152_mis_T_G	62	535	384
153_mis_T_A	6	53	31
153_mis_T_C	23	265	195
153_mis_T_G	228	2002	1633
154_mis_G_A	11	86	56
154_mis_G_C	0	36	37
154_mis_G_T	9	84	73
155_mis_C_A	17	140	115
155_mis_C_G	33	300	205
155_mis_C_T	40	359	282
156_mis_G_A	12	126	105
156_mis_G_C	10	85	65
156_mis_G_T	5	59	48
157_mis_C_A	33	419	348
157_mis_C_G	15	108	88
157_mis_C_T	5	71	50
158_mis_A_C	27	202	160
158_mis_A_G	73	897	645
158_mis_A_T	3	44	46
159_mis_G_A	15	73	44
159_mis_G_C	5	27	27
159_mis_G_T	55	506	329
160_mis_C_A	18	142	145
160_mis_C_G	28	347	224
160_mis_C_T	8	124	101
161_mis_C_A	36	408	267
161_mis_C_G	8	100	77
161_mis_C_T	6	84	76
162_mis_T_A	37	363	247
162_mis_T_C	18	190	168
162_mis_T_G	63	673	518
163_mis_G_A	19	186	123
163_mis_G_C	0	14	14
163_mis_G_T	19	156	116
164_mis_A_C	0	19	19
164_mis_A_G	16	160	123
164_mis_A_T	5	86	65
165_mis_A_C	0	17	11
165_mis_A_G	26	271	207
165_mis_A_T	6	34	41
166_mis_T_A	25	301	236
166_mis_T_C	9	96	97
166_mis_T_G	158	1562	1070
167_mis_G_A	20	191	175
167_mis_G_C	0	13	9
167_mis_G_T	0	36	29
168_mis_G_A	32	378	309
168_mis_G_C	3	26	28
168_mis_G_T	0	55	48
169_mis_C_A	23	245	187
169_mis_C_G	21	188	140
169_mis_C_T	20	288	228
170_mis_G_A	10	155	91
170_mis_G_C	6	27	26
170_mis_G_T	4	62	39
171_mis_A_C	57	500	408
171_mis_A_G	7	127	101
171_mis_A_T	5	73	68
172_mis_A_C	0	27	28
172_mis_A_G	17	193	133
172_mis_A_T	0	44	34
173_mis_T_A	16	146	130
173_mis_T_C	7	89	72
173_mis_T_G	69	568	450
174_mis_G_A	11	109	92
174_mis_G_C	0	34	22
174_mis_G_T	0	48	42
175_mis_G_A	11	112	108
175_mis_G_C	0	26	12
175_mis_G_T	50	417	347
176_mis_C_A	78	708	536
176_mis_C_G	28	293	167
176_mis_C_T	42	520	409
177_mis_G_A	10	128	99
177_mis_G_C	3	19	23
177_mis_G_T	4	90	69
178_mis_C_A	71	733	465
178_mis_C_G	13	154	108
178_mis_C_T	12	102	101
179_mis_T_A	12	200	149
179_mis_T_C	5	88	75
179_mis_T_G	32	403	332
180_mis_A_C	24	125	112
180_mis_A_G	5	41	44
180_mis_A_T	14	92	66
181_mis_A_C	11	128	98
181_mis_A_G	6	43	59
181_mis_A_T	10	62	44
182_mis_T_A	17	194	108
182_mis_T_C	7	56	46
182_mis_T_G	25	274	184
183_mis_A_C	15	142	127
183_mis_A_G	4	40	46
183_mis_A_T	8	68	60
184_mis_A_C	16	145	105
184_mis_A_G	8	81	80
184_mis_A_T	0	45	35
185_mis_G_A	13	141	108
185_mis_G_C	3	42	18
185_mis_G_T	14	147	110
186_mis_A_C	14	157	122
186_mis_A_G	5	66	74
186_mis_A_T	5	57	39
187_mis_T_A	19	187	152
187_mis_T_C	9	67	67
187_mis_T_G	28	268	201
188_mis_A_C	14	196	130
188_mis_A_G	7	41	56
188_mis_A_T	12	84	52
189_mis_T_A	14	120	122
189_mis_T_C	11	107	74
189_mis_T_G	33	219	165
190_mis_C_A	26	246	171
190_mis_C_G	0	18	9
190_mis_C_T	0	25	24
191_mis_A_C	33	267	205
191_mis_A_G	4	62	37
191_mis_A_T	6	67	63
192_mis_T_A	17	127	118
192_mis_T_C	25	155	136
192_mis_T_G	31	281	227
193_mis_C_A	8	105	78
193_mis_C_G	0	62	36
193_mis_C_T	0	20	20
194_mis_G_A	8	47	42
194_mis_G_C	6	64	30
194_mis_G_T	4	34	31
195_mis_G_A	8	83	62
195_mis_G_C	13	118	82
195_mis_G_T	17	174	135
196_mis_C_A	13	81	59
196_mis_C_G	28	246	242
196_mis_C_T	27	195	163
197_mis_T_A	4	28	15
197_mis_T_C	6	29	37
197_mis_T_G	21	165	114
198_mis_T_A	0	60	31
198_mis_T_C	3	64	42
198_mis_T_G	58	519	432
199_mis_T_A	0	19	17
199_mis_T_C	19	169	116
199_mis_T_G	20	230	173

## Raw table: miss_reads_by_ref_nt.

	s1	s2	s3
A	11089	185513	642747
C	61814	454411	1027101
G	59338	394848	524396
T	10714	122061	247384

## Raw table: miss_indexes_by_ref_nt.

	s1	s2	s3
A	2257	21655	67872
C	11780	51395	106854
G	11598	44664	55605
T	2271	15557	29241

## Raw table: miss_sequencer_by_ref_nt.

	s1	s2	s3
A	3264	28892	23544
C	2611	28669	22007
G	2028	20250	17008
T	3921	42299	34232

## Raw table: miss_reads_by_hit_nt.

	s1	s2	s3
A	59725	583633	768181
C	11818	82889	185317
G	10861	207526	696018
T	60551	282785	792112

## Raw table: miss_indexes_by_hit_nt.

	s1	s2	s3
A	11212	65291	80608
C	2431	10665	22026
G	2265	24716	74627
T	11998	32599	82311

## Raw table: miss_sequencer_by_hit_nt.

	s1	s2	s3
A	2286	24749	19533
C	3854	35111	29333
G	3731	41049	32521
T	1953	19201	15404

## Raw table: miss_reads_by_type.

	s1	s2	s3
A_C	6600	36402	80208
A_G	3424	131463	516538
A_T	1065	17648	46001
C_A	49857	261579	329363
C_G	1743	32557	93322
C_T	10214	160275	604416
G_A	8777	277538	359399
G_C	1289	12448	23302
G_T	49272	104862	141695
T_A	1091	44516	79419
T_C	3929	34039	81807
T_G	5694	43506	86158

## Raw table: miss_indexes_by_type.

	s1	s2	s3
A_C	1294	4516	9418
A_G	728	14896	53401
A_T	235	2243	5053
C_A	9305	29486	34851
C_G	342	3848	10038
C_T	2133	18061	61965
G_A	1685	30686	37225
G_C	283	1683	3087
G_T	9630	12295	15293
T_A	222	5119	8532
T_C	854	4466	9521
T_G	1195	5972	11188

## Raw table: miss_sequencer_by_type.

	s1	s2	s3
A_C	2381	18295	15010
A_G	659	7440	5942
A_T	224	3157	2592
C_A	1278	15254	11862
C_G	601	6072	4442
C_T	732	7343	5703
G_A	555	5215	4268
G_C	476	6334	5631
G_T	997	8701	7109
T_A	453	4280	3403
T_C	997	10482	8692
T_G	2471	27537	22137

## Raw table: miss_reads_by_trans.

	s1	s2	s3
transition	26344	603315	1562160
transversion	116611	553518	879468

## Raw table: miss_indexes_by_trans.

	s1	s2	s3
transition	5400	68109	162112
transversion	22506	65162	97460

## Raw table: miss_sequencer_by_trans.

	s1	s2	s3
transition	2943	30480	24605
transversion	8881	89630	72186

## Raw table: miss_reads_by_strength.

	s1	s2	s3
strong_strong	3032	45005	116624
strong_weak	118120	804254	1434873
weak_strong	19647	245410	764711
weak_weak	2156	62164	125420

## Raw table: miss_indexes_by_strength.

	s1	s2	s3
strong_strong	625	5531	13125
strong_weak	22753	90528	149334
weak_strong	4071	29850	83528
weak_weak	457	7362	13585

## Raw table: miss_sequencer_by_strength.

	s1	s2	s3
strong_strong	1077	12406	10073
strong_weak	3562	36513	28942
weak_strong	6508	63754	51781
weak_weak	677	7437	5995

## Raw table: insert_reads_by_position.

	s1	s2	s3
24	0	0	13
25	0	7	0
26	0	4	0
27	0	12	0
28	0	0	13
29	0	0	4
30	0	17	78
35	0	0	24
36	0	7	8
42	0	14	0
44	0	0	5
45	0	0	13
46	6	9	36
47	0	5	3
48	0	156	829
50	0	0	20
51	4	194	3465
52	0	0	144
55	0	0	256
58	0	0	3
59	0	0	7
61	0	0	3
62	0	3	0
69	0	0	5
72	0	0	483
81	0	0	64
91	0	72	698
92	6	191	219
93	0	0	36
97	0	260	753
100	0	23	0
105	0	0	8
110	0	0	4
120	0	0	4
123	0	0	320
124	0	0	4
126	7	0	0
130	0	0	5
132	0	10	0
134	4	0	0
137	0	0	10
138	0	0	4
142	0	0	31
144	0	0	90
148	0	0	20
149	0	12	0
151	0	12	0
154	0	64	0
156	0	6	0
171	7	0	4
174	7	0	0
177	0	0	8
182	6	0	0
190	0	0	6

## Raw table: insert_indexes_by_position.

	s2	s3
30	3	8
46	0	4
48	19	77
51	25	358
52	0	12
55	0	16
72	0	39
81	0	8
91	8	72
92	20	35
93	0	6
97	40	83
100	3	0
123	0	24
142	0	7
144	0	9
148	0	4
151	4	0
154	8	0

## Raw table: insert_sequencer_by_position.

	s2	s3
29	4	4
34	0	3
35	3	0
42	0	4
46	0	3
48	5	5
51	3	5
55	0	3
66	4	0
92	16	14
97	0	3
149	0	4
151	0	3
156	5	0

## Raw table: insert_reads_by_nt.

	s1	s2	s3
A	11	206	3845
C	19	239	713
G	11	266	1004
T	6	367	2138

## Raw table: insert_indexes_by_nt.

	s2	s3
A	25	382
C	23	70
G	31	89
T	51	221

## Raw table: insert_sequencer_by_nt.

	s2	s3
A	3	8
C	23	24
G	14	16
T	0	3

## Raw table: delete_reads_by_position.

s1	s2	s3

## Raw table: delete_indexes_by_position.

s1	s2	s3

## Raw table: delete_sequencer_by_position.

s1	s2	s3

## Raw table: delete_reads_by_nt.

s1	s2	s3

## Raw table: delete_indexes_by_nt.

s1	s2	s3

## Raw table: delete_sequencer_by_nt.

s1	s2	s3

5 Print raw plots

for (t in 1:length(triplets[["matrices"]])) {
  message("Raw table: ", table_name, ".")
  print(data_plots[["matrices"]][t])
}

## Raw table: delete_sequencer_by_nt.

## Error in print(data_plots[["matrices"]][t]): object 'data_plots' not found

6 Print normalized tables

for (t in 1:length(triplets[["normalized"]])) {
  table_name <- names(triplets[["normalized"]])[t]
  message("Normalized table: ", table_name, ".")
  print(knitr::kable(triplets[["normalized"]][t]))
}

## Normalized table: miss_reads_by_position.

	s1	s2	s3
24	7568.8	6045.0	8502.5
25	7247.0	8513.8	4927.9
26	10143.1	14563.0	11430.9
27	3140.8	3723.1	4505.6
28	3777.4	5726.8	6529.7
29	12619.4	10780.3	7280.8
30	10171.0	6734.8	6507.5
31	636.6	937.0	1522.8
32	909.4	516.9	533.7
33	741.5	941.4	2075.7
34	5708.1	4914.3	7372.1
35	3952.3	7430.6	10348.8
36	2217.5	6549.8	7663.7
37	7953.6	5349.1	8548.0
38	7107.1	6685.5	8260.5
39	8674.1	12459.9	8333.4
40	2623.2	3326.3	3560.7
41	6064.8	3577.9	5740.8
42	8002.5	9790.5	5673.7
43	3357.7	4651.5	4463.0
44	14452.1	8654.7	5930.5
45	3735.4	5554.0	12417.5
46	3294.7	11137.3	17716.5
47	5862.0	6872.2	6290.1
48	8107.4	8821.5	7138.7
49	10919.5	13231.8	7631.4
50	6463.6	10605.7	20476.1
51	4176.1	8970.2	12089.9
52	454.7	5898.0	12369.6
53	804.4	7381.4	12960.2
54	19152.9	12446.0	11789.7
55	6715.4	10623.8	9909.0
56	10394.9	6020.7	5339.1
57	20873.7	9501.8	5381.7
58	5183.4	5477.9	4320.1
59	20111.2	11979.3	6305.2
60	24958.9	12732.2	6514.5
61	9128.7	8510.3	10372.6
62	8548.1	10559.9	5563.5
63	1007.3	4951.4	4846.8
64	762.5	2181.8	1868.8
65	4239.1	8210.3	11928.1
66	2441.3	10418.1	18841.1
67	3952.3	6525.6	5443.9
68	11507.1	6872.2	5024.5
69	1350.1	2369.4	2121.5
70	1392.0	3341.9	6526.4
71	3539.6	6120.2	8914.1
72	377.7	341.4	1082.5
73	195.9	1134.1	888.3
74	468.7	4181.2	5020.4
75	188.9	5001.6	9301.6
76	664.5	3271.9	2809.2
77	8303.3	6274.9	6699.6
78	17823.8	8958.1	5928.8
79	8065.5	6637.1	8038.5
80	4896.6	3908.9	4725.5
81	503.7	727.8	1445.3
82	202.9	1845.6	1803.7
83	13220.9	7107.3	4213.2
84	10185.0	6453.8	10132.2
85	664.5	1811.8	3136.8
86	13731.6	8909.7	5869.4
87	10660.7	9102.4	12219.7
88	811.4	2768.8	3114.3
89	2511.3	9124.9	10214.9
90	587.6	2436.0	5399.3
91	678.5	3382.5	2332.9
92	5645.1	4623.8	4371.3
93	6498.5	7316.5	6773.8
94	10555.8	8991.8	5065.9
95	12080.7	6213.5	3909.7
96	9856.2	7296.6	4354.9
97	566.6	1978.7	1352.4
98	447.7	1303.6	1461.3
99	461.7	708.8	407.9
100	8275.3	21427.5	14412.9
101	9618.4	7539.5	3795.4
102	10534.8	4415.5	5142.9
103	5036.6	3760.3	2729.7
104	447.7	1733.2	2301.7
105	13332.9	8426.5	5871.5
106	7156.1	8557.8	9233.2
107	601.6	3154.3	2013.0
108	7799.7	6497.9	3204.4
109	9996.2	7183.4	4735.4
110	13144.0	8610.6	11025.8
111	16627.6	9675.6	4306.6
112	4742.8	4582.3	4224.6
113	202.9	3500.1	6424.0
114	538.6	6376.0	12583.8
115	1874.7	5194.4	4587.1
116	2777.1	4021.3	6454.3
117	8751.0	8323.6	4223.0
118	9478.5	8770.5	9877.0
119	8002.5	8440.3	3689.3
120	629.6	3072.2	5051.5
121	1098.2	6347.5	11421.1
122	2224.5	4468.2	3990.0
123	1000.3	4929.8	9933.9
124	5204.4	5936.0	3951.1
125	18495.3	8919.2	4866.0
126	21664.2	9781.0	10663.4
127	10094.1	5057.8	3992.8
128	14277.2	9020.3	6071.8
129	18474.3	11738.9	5855.1
130	9471.5	10887.5	10785.0
131	3819.4	4896.1	6138.1
132	5253.4	6799.6	10160.8
133	10527.8	4967.0	5065.9
134	5435.3	7476.4	2768.6
135	1462.0	3039.3	4805.4
136	1084.3	1822.2	2334.9
137	4910.6	5097.5	4608.8
138	12423.5	6819.5	4157.1
139	5980.9	7313.9	9227.9
140	4483.9	4036.9	5312.4
141	7324.0	5065.6	4489.6
142	3070.9	2652.1	2770.3
143	3126.9	4098.3	3794.2
144	4973.6	5254.0	5941.9
145	5708.1	5686.2	4441.3
146	10926.5	6026.8	5576.2
147	482.7	1135.9	2206.3
148	818.4	2807.7	4753.4
149	4861.7	7491.1	9133.7
150	1077.3	2895.0	3510.8
151	8289.3	7654.5	3931.4
152	1371.1	3445.6	3470.2
153	3091.9	3347.1	3480.5
154	7624.8	6338.9	3267.5
155	8688.0	8553.5	8337.5
156	11898.8	8795.6	5306.3
157	8548.1	8485.2	10474.6
158	2280.4	4004.0	4607.6
159	9275.6	6481.5	4754.6
160	6631.5	6827.3	10691.2
161	5931.9	3877.0	4559.7
162	5966.9	4196.8	2808.4
163	6939.2	8159.3	3727.0
164	433.7	2548.3	5325.1
165	384.7	4804.5	11686.9
166	2476.3	4684.3	3718.8
167	9366.6	6414.1	3971.9
168	10492.8	8262.2	4645.3
169	8772.0	7895.7	7810.8
170	5365.3	7605.2	4112.4
171	1189.2	3997.1	5544.3
172	622.6	7301.0	14883.9
173	1000.3	4389.6	3112.7
174	6617.5	7271.6	4130.9
175	10366.9	10135.4	5095.8
176	15431.4	8820.6	8924.8
177	11982.8	10084.4	3600.9
178	6260.7	7525.7	8483.7
179	1238.2	1597.5	1338.5
180	524.6	681.2	1650.5
181	489.7	1132.4	2986.5
182	741.5	929.3	1209.4
183	699.5	644.0	1139.0
184	349.8	779.7	1925.4
185	1056.3	791.8	1905.3
186	671.5	833.3	2545.0
187	1042.3	1058.9	1467.1
188	909.4	861.8	2333.7
189	818.4	1051.1	1131.6
190	559.6	912.8	1240.2
191	755.5	837.6	1273.7
192	1203.2	1109.9	1285.6
193	237.8	1017.4	1170.5
194	363.8	691.5	739.7
195	1280.1	2033.1	1880.7
196	433.7	1209.3	3317.9
197	538.6	534.2	607.4
198	1601.9	1232.7	2147.3
199	860.4	1423.7	1739.4

## Normalized table: miss_indexes_by_position.

	s1	s2	s3
24	7059.4	6483.0	7978.5
25	7847.8	8313.9	5000.5
26	11072.9	14564.3	11291.7
27	3834.3	4419.6	4931.2
28	4156.8	5882.8	6730.3
29	12040.4	11165.2	7208.0
30	11144.6	7270.9	7115.6
31	824.2	840.4	1336.8
32	967.5	532.7	689.6
33	1039.2	930.4	1960.9
34	6844.4	5987.8	7678.0
35	4586.8	7518.5	10424.9
36	2472.6	7270.9	8729.8
37	7991.1	5837.7	8806.8
38	6091.9	6655.6	8128.8
39	9639.5	12703.4	8679.7
40	3153.4	4111.9	3998.9
41	6378.6	3789.3	5670.9
42	8922.8	9702.0	5944.4
43	3762.6	5342.5	5204.7
44	12362.9	8306.4	5967.5
45	4336.0	5882.8	11861.8
46	3045.9	10542.4	16219.0
47	6235.2	7788.6	7119.4
48	8528.6	9071.7	6526.1
49	10177.0	12508.3	7165.6
50	6880.2	11022.7	19736.3
51	4551.0	9476.9	11858.0
52	573.4	5410.0	11542.1
53	860.0	6880.7	12281.8
54	18168.1	11427.8	11295.5
55	6916.1	11270.3	11145.3
56	9603.7	5530.1	5062.2
57	21429.1	9079.2	5235.5
58	5912.7	7240.9	5432.0
59	18705.7	10992.6	6445.2
60	25227.5	11570.4	6568.5
61	9102.0	8501.5	10405.6
62	8922.8	10017.2	5501.4
63	1254.2	6167.9	6021.5
64	824.2	2198.5	1918.5
65	5124.3	8103.8	11888.8
66	2580.1	10632.5	18079.8
67	4228.5	6242.9	5208.6
68	10678.7	5882.8	4723.2
69	1146.7	2416.1	2180.5
70	1290.0	3609.2	6514.6
71	3726.8	6017.8	8887.7
72	501.7	435.2	1078.7
73	179.2	1005.5	901.5
74	501.7	3526.6	5062.2
75	0.0	4929.8	8749.0
76	680.9	3076.4	2789.2
77	7632.8	6122.9	6722.6
78	17021.4	8479.0	5593.8
79	8564.5	6032.8	7373.7
80	4694.3	3774.3	4307.1
81	573.4	840.4	1548.7
82	143.3	1748.3	1880.0
83	13402.1	7030.8	4318.6
84	8385.3	6265.4	9577.3
85	895.9	2018.4	3004.9
86	13402.1	8929.2	5362.7
87	9711.2	8846.6	11526.7
88	967.5	2513.7	3174.5
89	2687.6	9079.2	9638.9
90	609.2	2551.2	5524.5
91	573.4	3068.9	2392.4
92	5841.0	4412.1	4168.4
93	6736.9	7023.3	6156.3
94	10642.9	8186.3	4788.7
95	11037.1	6445.5	3883.3
96	9962.0	6925.7	4626.8
97	501.7	1808.3	1371.5
98	573.4	1478.2	1460.1
99	430.0	735.3	550.9
100	8349.5	20312.0	14192.6
101	10356.2	7496.0	4145.3
102	10248.7	4524.6	5378.1
103	5339.4	3991.9	2951.0
104	609.2	1665.8	2199.8
105	13043.8	7698.6	5478.2
106	6844.4	7676.1	9199.8
107	716.7	2903.9	2103.5
108	8062.8	6295.4	3128.2
109	9747.0	6798.2	4661.5
110	12936.3	8944.2	10929.5
111	16233.1	9056.7	4276.3
112	4945.2	4982.3	4788.7
113	250.8	3714.2	6429.8
114	537.5	6355.5	12293.3
115	2257.6	5462.6	4873.4
116	2938.4	4014.4	6295.0
117	9066.2	8028.8	4260.9
118	9424.5	8726.6	9569.6
119	8242.0	8253.9	3594.4
120	716.7	3309.0	5004.4
121	1039.2	6265.4	11041.3
122	1612.6	4284.5	3883.3
123	1146.7	4562.1	9411.6
124	5841.0	6242.9	3998.9
125	18347.3	8921.7	4931.2
126	19171.5	9762.1	10332.4
127	10212.9	4959.8	4075.9
128	13653.0	8704.1	5778.7
129	19171.5	10482.4	5767.2
130	9460.3	10549.9	10166.7
131	3977.6	5342.5	6649.4
132	5088.5	6032.8	9777.6
133	9137.8	5072.4	4973.6
134	5088.5	7691.1	2835.4
135	1576.7	2993.9	4800.2
136	1254.2	1980.9	2588.9
137	4694.3	4959.8	4426.5
138	12255.4	7015.8	4345.6
139	5626.0	6873.2	9288.4
140	4443.5	4134.4	5015.9
141	7238.6	4914.8	4226.2
142	3045.9	3016.4	3228.4
143	3296.8	4689.7	4418.8
144	5590.2	5117.4	5751.8
145	5375.2	5192.4	4441.9
146	9460.3	5845.2	5732.5
147	501.7	1245.6	2149.7
148	1039.2	2791.3	4746.3
149	4730.2	7533.5	8787.5
150	1039.2	2611.2	3767.7
151	8492.8	7511.0	3756.2
152	1361.7	3691.7	3405.6
153	3368.5	3849.3	4079.8
154	8062.8	6107.9	3193.7
155	9711.2	8418.9	8279.0
156	11861.2	8824.1	5293.3
157	8026.9	9034.2	9754.5
158	2150.1	4194.5	4734.7
159	9675.3	7105.8	5216.3
160	7131.1	7293.4	10320.8
161	5769.4	3856.8	4422.7
162	5841.0	4637.2	3174.5
163	6378.6	7586.0	3763.9
164	537.5	2686.3	5127.7
165	358.3	4884.8	11542.1
166	3010.1	5425.0	4210.8
167	9962.0	6738.2	4222.3
168	11287.9	8238.9	4927.3
169	9066.2	7646.1	8151.9
170	5661.9	7833.7	4126.0
171	1325.9	4014.4	5859.6
172	609.2	7248.4	14577.8
173	1039.2	4524.6	3205.3
174	5339.4	6865.7	4052.8
175	11108.7	10384.9	5062.2
176	14405.5	9386.9	9396.2
177	11753.7	9522.0	3802.4
178	6414.4	7338.4	8679.7
179	1325.9	1913.4	1675.8
180	501.7	892.9	1668.1
181	394.2	1185.6	3105.1
182	645.0	1103.0	1340.7
183	573.4	862.9	1321.4
184	394.2	877.9	2145.8
185	1075.0	1013.0	2111.2
186	752.5	937.9	2550.4
187	1039.2	1223.1	1656.6
188	824.2	975.5	2442.5
189	752.5	1275.6	1429.3
190	609.2	1028.0	1379.2
191	752.5	1013.0	1460.1
192	1254.2	1463.2	1637.3
193	215.0	1088.0	1356.1
194	250.8	877.9	905.3
195	1325.9	2198.5	2169.0
196	430.0	1268.1	3247.7
197	430.0	592.8	758.9
198	1720.1	1620.8	2550.4
199	967.5	1335.6	1822.2

## Normalized table: miss_sequencer_by_position.

	s1	s2	s3
24	1184.0	1540.3	1642.7
25	3890.4	2872.4	2768.9
26	6512.2	8550.5	10093.9
27	18437.1	17575.6	19041.0
28	2621.8	4079.6	3605.7
29	5328.1	4379.3	4380.6
30	3890.4	20464.6	21551.6
31	676.6	1290.5	1188.1
32	761.2	949.1	1115.8
33	2960.1	2031.5	2014.7
34	23765.2	13204.6	13844.3
35	6173.9	6402.5	6612.2
36	11079.2	27999.3	31480.2
37	24695.5	14595.0	15683.3
38	2198.9	6460.7	6374.6
39	13954.7	19815.2	21964.9
40	23342.4	21255.5	21479.3
41	1860.6	2947.3	2582.9
42	3890.4	9724.4	10507.2
43	25287.6	24935.5	25839.2
44	4313.3	6327.5	6705.2
45	35521.0	18899.3	18948.0
46	2452.6	3979.7	4081.0
47	26471.6	27100.2	29093.6
48	5159.0	4795.6	5010.8
49	2452.6	4287.7	4204.9
50	8119.1	4096.2	4618.2
51	5412.7	9774.4	10062.9
52	3129.2	2889.0	2758.5
53	5666.4	3205.4	3285.4
54	16407.3	10756.8	10476.2
55	2283.5	22304.6	22037.2
56	2114.3	1165.6	1260.4
57	3636.7	1648.5	1684.0
58	9641.4	16126.9	17160.7
59	4989.9	11039.9	11550.7
60	30446.5	12571.8	13668.6
61	2960.1	2447.8	2789.5
62	6089.3	6993.6	7314.7
63	4059.5	25435.0	24795.7
64	3890.4	2447.8	2489.9
65	30277.4	18433.1	19536.9
66	2875.5	5853.0	5496.4
67	1691.5	2081.4	2097.3
68	7273.3	3929.7	3988.0
69	2537.2	1623.5	1653.0
70	4397.8	3971.4	3874.3
71	1099.5	999.1	1177.8
72	1606.9	1323.8	1312.1
73	1184.0	1282.2	1374.1
74	1860.6	2314.5	2272.9
75	1522.3	1440.3	1312.1
76	2537.2	2389.5	2655.2
77	1184.0	915.8	909.2
78	2283.5	2148.0	2169.6
79	845.7	1032.4	1188.1
80	1184.0	857.5	898.8
81	1437.8	2081.4	1983.7
82	1437.8	1648.5	1756.4
83	2283.5	2156.4	2035.3
84	1353.2	1815.0	1973.3
85	2114.3	2223.0	2190.3
86	1691.5	1873.3	1942.3
87	1860.6	1115.6	991.8
88	3890.4	3796.5	4070.6
89	676.6	957.5	1064.1
90	2198.9	2772.5	2861.8
91	3213.8	2314.5	2582.9
92	1099.5	741.0	847.2
93	253.7	1340.4	1312.1
94	676.6	774.3	692.2
95	676.6	591.1	805.9
96	1522.3	1457.0	1343.1
97	845.7	1357.1	1477.4
98	1691.5	1798.4	1963.0
99	2114.3	1548.6	1735.7
100	1099.5	790.9	826.5
101	3552.1	2755.8	2820.5
102	2452.6	2214.6	2262.6
103	930.3	1024.1	1126.1
104	1437.8	1432.0	1580.7
105	845.7	1082.3	1363.8
106	507.4	1007.4	1219.1
107	2706.4	2039.8	2458.9
108	592.0	1198.9	1508.4
109	2452.6	1698.4	1859.7
110	11163.7	5761.4	5341.4
111	2368.1	2064.8	2221.3
112	26302.4	22562.7	22388.4
113	1353.2	1765.0	1704.7
114	1353.2	1731.7	1828.7
115	16661.0	15011.2	14722.4
116	5497.3	4887.2	5165.8
117	1268.6	1315.5	1353.4
118	6512.2	6710.5	5713.3
119	2114.3	1382.1	1384.4
120	3975.0	4254.4	4132.6
121	4228.7	4629.1	4297.9
122	1184.0	1340.4	1281.1
123	3298.4	3971.4	3605.7
124	5835.6	5037.0	5548.0
125	9726.0	7085.2	6601.9
126	13447.2	14037.1	8637.2
127	4651.6	5586.5	5031.5
128	10064.3	7501.5	7345.7
129	1691.5	3113.8	3295.8
130	9810.6	9541.3	9804.6
131	26133.3	23320.3	21448.3
132	4482.4	4379.3	4804.2
133	2621.8	2647.6	2489.9
134	2537.2	1898.3	2097.3
135	5328.1	5611.5	5837.3
136	8964.8	6643.9	6798.2
137	3890.4	3680.0	3357.8
138	2960.1	2980.6	3068.5
139	7104.2	6111.1	6095.6
140	7949.9	7176.8	7779.6
141	3382.9	3630.0	3481.7
142	17083.9	14769.8	13875.3
143	26979.0	24003.0	22843.0
144	2621.8	3646.7	3502.4
145	6258.5	5553.2	5703.0
146	7357.9	7659.6	6880.8
147	1860.6	2281.2	2118.0
148	3467.5	4529.2	4070.6
149	3298.4	2847.4	2830.8
150	4482.4	5078.7	4473.6
151	2198.9	1798.4	1849.3
152	6512.2	5719.8	5527.4
153	21735.5	19315.6	19206.3
154	1691.5	1715.1	1715.0
155	7611.6	6652.2	6219.6
156	2283.5	2247.9	2252.3
157	4482.4	4978.8	5021.1
158	8711.1	9516.3	8792.1
159	6343.0	5045.4	4132.6
160	4567.0	5103.7	4855.8
161	4228.7	4928.8	4339.2
162	9979.7	10207.3	9639.3
163	3213.8	2963.9	2613.9
164	1776.0	2206.3	2138.6
165	2706.4	2680.9	2675.9
166	16238.2	16310.0	14495.1
167	1691.5	1998.2	2200.6
168	2960.1	3821.5	3977.6
169	5412.7	6002.8	5734.0
170	1691.5	2031.5	1611.7
171	5835.6	5828.0	5961.3
172	1437.8	2198.0	2014.7
173	7780.8	6685.5	6736.2
174	930.3	1590.2	1611.7
175	5159.0	4620.8	4824.8
176	12516.9	12663.4	11488.7
177	1437.8	1973.2	1973.3
178	8119.1	8234.1	6963.5
179	4144.1	5753.1	5744.3
180	3636.7	2148.0	2293.6
181	2283.5	1939.9	2076.6
182	4144.1	4362.7	3492.1
183	2283.5	2081.4	2407.2
184	2029.8	2256.3	2272.9
185	2537.2	2747.5	2438.2
186	2029.8	2331.2	2427.9
187	4736.1	4346.0	4339.2
188	2790.9	2672.6	2458.9
189	4905.3	3713.3	3729.7
190	2198.9	2406.1	2107.6
191	3636.7	3297.0	3151.1
192	6173.9	4687.4	4969.5
193	676.6	1556.9	1384.4
194	1522.3	1207.2	1064.1
195	3213.8	3122.1	2882.5
196	5751.0	4346.0	4793.8
197	2621.8	1848.3	1715.0
198	5159.0	5353.4	5217.4
199	3298.4	3480.1	3161.5

## Normalized table: miss_reads_by_string.

	s1	s2	s3
024_mis_C_A	5903.96	3992.80	2610.96
024_mis_C_G	0.00	682.03	1082.88
024_mis_C_T	1664.86	1370.12	4808.68
025_mis_C_A	5561.19	5097.54	2762.91
025_mis_C_G	251.83	663.02	433.73
025_mis_C_T	1434.02	2753.21	1731.22
026_mis_G_A	1357.07	10871.92	8767.51
026_mis_G_C	503.65	977.67	943.63
026_mis_G_T	8282.33	2713.44	1719.75
027_mis_T_A	27.98	553.23	1394.56
027_mis_T_C	2840.05	1524.85	1641.12
027_mis_T_G	272.81	1645.01	1469.92
028_mis_C_A	2574.24	4027.37	1990.88
028_mis_C_G	97.93	209.19	357.96
028_mis_C_T	1105.24	1490.28	4180.82
029_mis_G_A	930.36	8737.65	5529.10
029_mis_G_C	797.45	398.50	333.79
029_mis_G_T	10891.54	1644.14	1417.91
030_mis_T_A	76.95	44.95	233.04
030_mis_T_C	1203.18	1356.29	1691.08
030_mis_T_G	8890.91	5333.53	4583.42
031_mis_T_A	27.98	439.99	692.57
031_mis_T_C	230.84	405.42	716.33
031_mis_T_G	377.74	91.63	113.86
032_mis_T_A	27.98	101.14	72.90
032_mis_T_C	748.49	356.14	422.26
032_mis_T_G	132.91	59.65	38.50
033_mis_T_A	258.82	167.70	1266.37
033_mis_T_C	482.67	730.44	692.98
033_mis_T_G	0.00	43.22	116.32
034_mis_A_C	2231.47	934.45	844.52
034_mis_A_G	1944.67	2498.20	5248.96
034_mis_A_T	1531.95	1481.63	1278.66
035_mis_C_A	3098.88	3078.23	1877.03
035_mis_C_G	0.00	0.00	256.39
035_mis_C_T	853.42	4352.40	8215.42
036_mis_A_C	1371.06	3733.47	4621.51
036_mis_A_G	825.43	2506.84	2584.34
036_mis_A_T	20.99	309.47	457.89
037_mis_A_C	4469.94	2444.61	1946.24
037_mis_A_G	3448.64	2579.46	6311.77
037_mis_A_T	34.98	325.03	289.97
038_mis_C_A	5757.06	4001.44	3070.90
038_mis_C_G	216.85	140.04	399.32
038_mis_C_T	1133.22	2544.01	4790.25
039_mis_G_A	1685.85	7852.47	4182.05
039_mis_G_C	454.69	2330.50	2170.68
039_mis_G_T	6533.52	2276.91	1980.65
040_mis_T_A	97.93	99.41	551.68
040_mis_T_C	2343.39	1377.04	1501.46
040_mis_T_G	181.88	1849.88	1507.60
041_mis_C_A	5666.12	2638.24	2911.17
041_mis_C_G	125.91	89.90	710.59
041_mis_C_T	272.81	849.73	2119.08
042_mis_G_A	1839.74	7077.08	3734.39
042_mis_G_C	342.77	842.82	1145.55
042_mis_G_T	5820.01	1870.62	793.73
043_mis_T_A	132.91	584.35	909.64
043_mis_T_C	370.75	962.11	714.28
043_mis_T_G	2854.05	3105.03	2839.09
044_mis_G_A	545.63	4871.06	3833.51
044_mis_G_C	48.97	115.83	204.78
044_mis_G_T	13857.51	3667.77	1892.18
045_mis_A_C	3420.66	1899.15	1976.55
045_mis_A_G	160.89	3111.94	10156.75
045_mis_A_T	153.89	542.86	284.24
046_mis_C_A	2462.31	4306.59	1989.66
046_mis_C_G	55.96	1008.79	1798.39
046_mis_C_T	776.47	5821.93	13928.41
047_mis_T_A	461.68	2394.47	1720.57
047_mis_T_C	1462.00	3288.29	3463.67
047_mis_T_G	3938.30	1189.45	1105.82
048_mis_G_A	720.51	6493.59	5756.41
048_mis_G_C	0.00	34.58	26.62
048_mis_G_T	7386.94	2293.33	1355.65
049_mis_G_A	1245.15	10777.70	5732.24
049_mis_G_C	545.63	332.81	178.57
049_mis_G_T	9128.75	2121.31	1720.57
050_mis_G_A	2700.15	9799.17	19715.94
050_mis_G_C	328.77	264.52	130.24
050_mis_G_T	3434.65	542.00	629.91
051_mis_A_C	349.76	369.98	370.65
051_mis_A_G	3679.48	8416.95	11595.54
051_mis_A_T	146.90	183.26	123.69
052_mis_A_C	314.78	248.09	589.77
052_mis_A_G	139.90	5359.46	11568.92
052_mis_A_T	0.00	290.45	210.92
053_mis_A_C	601.59	506.56	889.16
053_mis_A_G	125.91	6832.45	11613.56
053_mis_A_T	76.95	42.36	457.48
054_mis_A_C	19047.95	6475.44	2387.34
054_mis_A_G	104.93	5960.24	9034.14
054_mis_A_T	0.00	10.37	368.20
055_mis_C_A	5722.08	8247.52	5052.37
055_mis_C_G	0.00	761.56	398.91
055_mis_C_T	993.32	1614.75	4457.68
056_mis_C_A	9387.57	3849.30	2876.36
056_mis_C_G	734.50	299.96	403.83
056_mis_C_T	272.81	1871.49	2058.87
057_mis_C_A	9128.75	5924.80	3043.87
057_mis_C_G	0.00	221.29	511.13
057_mis_C_T	11744.95	3355.71	1826.65
058_mis_T_A	132.91	1552.51	1316.74
058_mis_T_C	4295.06	3531.19	2608.91
058_mis_T_G	755.48	394.18	394.41
059_mis_G_A	8394.25	8274.31	3770.44
059_mis_G_C	167.88	209.19	167.51
059_mis_G_T	11549.09	3495.75	2367.27
060_mis_G_A	104.93	6735.63	2515.94
060_mis_G_C	1979.64	1187.73	982.95
060_mis_G_T	22874.33	4808.82	3015.61
061_mis_C_A	8485.19	5082.84	2231.71
061_mis_C_G	377.74	841.09	1408.08
061_mis_C_T	265.82	2586.37	6732.80
062_mis_G_A	1287.12	7791.10	3537.80
062_mis_G_C	48.97	632.76	664.72
062_mis_G_T	7212.06	2136.00	1360.98
063_mis_T_A	20.99	376.03	681.10
063_mis_T_C	230.84	575.71	824.45
063_mis_T_G	755.48	3999.71	3341.21
064_mis_T_A	223.85	1230.95	788.41
064_mis_T_C	496.66	926.67	961.24
064_mis_T_G	41.97	24.20	119.18
065_mis_A_C	3161.83	1339.87	1503.51
065_mis_A_G	132.91	4665.32	7807.50
065_mis_A_T	944.35	2205.16	2617.11
066_mis_C_A	755.48	2746.29	1942.97
066_mis_C_G	0.00	619.80	1140.22
066_mis_C_T	1685.85	7052.01	15757.93
067_mis_C_A	2476.30	3747.30	2243.18
067_mis_C_G	0.00	299.96	208.06
067_mis_C_T	1475.99	2478.32	2992.68
068_mis_C_A	10226.99	5078.52	2967.69
068_mis_C_G	0.00	405.42	504.99
068_mis_C_T	1280.12	1388.27	1551.83
069_mis_A_C	482.67	650.05	343.21
069_mis_A_G	867.41	866.16	1048.89
069_mis_A_T	0.00	853.19	729.43
070_mis_A_C	853.42	229.07	432.09
070_mis_A_G	426.71	2865.58	5902.21
070_mis_A_T	111.92	247.23	192.09
071_mis_C_A	2266.45	2028.81	1629.65
071_mis_C_G	0.00	714.02	702.81
071_mis_C_T	1273.13	3377.32	6581.67
072_mis_T_A	0.00	152.14	353.04
072_mis_T_C	195.87	146.95	673.32
072_mis_T_G	181.88	42.36	56.11
073_mis_T_A	69.95	723.53	305.53
073_mis_T_C	125.91	344.91	443.15
073_mis_T_G	0.00	65.70	139.66
074_mis_A_C	139.90	920.62	303.49
074_mis_A_G	111.92	2871.63	4064.50
074_mis_A_T	216.85	388.99	652.43
075_mis_A_C	125.91	389.86	759.74
075_mis_A_G	41.97	4119.87	8271.94
075_mis_A_T	20.99	491.86	269.90
076_mis_T_A	405.72	2334.82	1322.48
076_mis_T_C	258.82	868.75	1366.71
076_mis_T_G	0.00	68.29	120.00
077_mis_C_A	6911.27	5028.38	3405.11
077_mis_C_G	41.97	273.16	351.00
077_mis_C_T	1350.08	973.35	2943.53
078_mis_G_A	503.65	5468.38	3093.43
078_mis_G_C	97.93	69.15	135.57
078_mis_G_T	17222.20	3420.55	2699.84
079_mis_C_A	7743.70	3390.29	1548.97
079_mis_C_G	0.00	407.15	910.46
079_mis_C_T	321.78	2839.65	5579.06
080_mis_C_A	4155.15	2076.36	1630.47
080_mis_C_G	97.93	29.39	127.78
080_mis_C_T	643.56	1803.20	2967.28
081_mis_T_A	188.87	335.40	619.67
081_mis_T_C	314.78	282.67	587.31
081_mis_T_G	0.00	109.78	238.37
082_mis_T_A	48.97	1073.62	1121.38
082_mis_T_C	97.93	682.03	617.62
082_mis_T_G	55.96	89.90	64.71
083_mis_G_A	496.66	4813.14	2350.07
083_mis_G_C	223.85	85.58	70.04
083_mis_G_T	12500.44	2208.62	1793.07
084_mis_C_A	9030.81	2568.22	1580.09
084_mis_C_G	104.93	136.58	467.72
084_mis_C_T	1049.28	3749.03	8084.36
085_mis_A_C	0.00	146.09	437.41
085_mis_A_G	664.54	994.96	2230.07
085_mis_A_T	0.00	670.80	469.36
086_mis_G_A	5211.43	7054.61	4205.80
086_mis_G_C	314.78	129.66	204.37
086_mis_G_T	8205.38	1725.40	1459.27
087_mis_C_A	10143.05	6022.48	3196.64
087_mis_C_G	62.96	1391.73	1493.68
087_mis_C_T	454.69	1688.23	7529.40
088_mis_A_C	300.79	374.30	373.93
088_mis_A_G	279.81	1926.81	2243.18
088_mis_A_T	230.84	467.66	497.21
089_mis_C_A	1468.99	3569.23	2764.96
089_mis_C_G	0.00	818.61	797.83
089_mis_C_T	1042.29	4737.07	6652.12
090_mis_A_C	202.86	574.85	821.17
090_mis_A_G	258.82	1696.01	3811.39
090_mis_A_T	125.91	165.11	766.70
091_mis_T_A	104.93	2734.19	1206.16
091_mis_T_C	524.64	605.96	1063.22
091_mis_T_G	48.97	42.36	63.48
092_mis_C_A	4581.86	2747.16	1421.18
092_mis_C_G	0.00	411.47	319.05
092_mis_C_T	1063.27	1465.21	2631.03
093_mis_C_A	5554.20	5037.03	4465.05
093_mis_C_G	174.88	879.99	439.46
093_mis_C_T	769.47	1399.51	1869.24
094_mis_C_A	10003.15	7900.88	2529.46
094_mis_C_G	62.96	172.89	375.16
094_mis_C_T	489.66	918.02	2161.26
095_mis_C_A	11640.03	5349.95	2756.77
095_mis_C_G	0.00	256.74	317.41
095_mis_C_T	440.70	606.83	835.51
096_mis_C_A	8883.91	5569.52	1967.54
096_mis_C_G	0.00	83.85	82.73
096_mis_C_T	972.33	1643.28	2304.61
097_mis_T_A	62.96	908.51	1123.43
097_mis_T_C	503.65	802.19	136.79
097_mis_T_G	0.00	267.97	92.15
098_mis_T_A	139.90	879.12	851.89
098_mis_T_C	146.90	388.13	553.73
098_mis_T_G	160.89	36.31	55.70
099_mis_T_A	20.99	101.14	106.90
099_mis_T_C	384.74	582.63	276.45
099_mis_T_G	55.96	25.07	24.57
100_mis_C_A	6428.60	3292.61	1577.23
100_mis_C_G	90.94	19.02	40.55
100_mis_C_T	1755.80	18115.84	12795.15
101_mis_G_A	1175.19	4931.57	2557.72
101_mis_G_C	419.71	149.55	140.07
101_mis_G_T	8023.50	2458.44	1097.63
102_mis_C_A	8681.05	2597.61	1204.52
102_mis_C_G	90.94	112.38	53.65
102_mis_C_T	1762.79	1705.52	3884.70
103_mis_C_A	3966.28	2588.96	1248.35
103_mis_C_G	0.00	81.26	124.10
103_mis_C_T	1070.27	1090.05	1357.29
104_mis_A_C	104.93	439.13	191.68
104_mis_A_G	237.84	765.02	1365.07
104_mis_A_T	104.93	529.03	744.99
105_mis_G_A	454.69	5174.47	3275.68
105_mis_G_C	111.92	14.70	19.25
105_mis_G_T	12766.26	3237.29	2576.56
106_mis_C_A	5659.12	5846.13	2945.99
106_mis_C_G	0.00	700.19	973.53
106_mis_C_T	1496.97	2011.53	5313.67
107_mis_T_A	76.95	2544.88	1244.66
107_mis_T_C	279.81	177.21	237.14
107_mis_T_G	244.83	432.21	531.20
108_mis_G_A	538.63	4687.80	2123.17
108_mis_G_C	195.87	162.51	26.21
108_mis_G_T	7065.16	1647.60	1055.03
109_mis_G_A	468.68	3884.74	2913.63
109_mis_G_C	62.96	158.19	37.68
109_mis_G_T	9464.52	3140.47	1784.06
110_mis_C_A	8667.06	4495.03	2326.32
110_mis_C_G	1427.02	844.55	673.32
110_mis_C_T	3049.91	3271.00	8026.20
111_mis_G_A	5987.90	7335.54	2878.82
111_mis_G_C	55.96	161.65	90.92
111_mis_G_T	10583.75	2178.36	1336.81
112_mis_T_A	195.87	1010.52	894.89
112_mis_T_C	1727.82	1058.06	874.42
112_mis_T_G	2819.07	2513.76	2455.33
113_mis_A_C	0.00	95.09	429.63
113_mis_A_G	181.88	2742.83	5305.48
113_mis_A_T	20.99	662.15	688.88
114_mis_A_C	104.93	707.97	927.25
114_mis_A_G	167.88	5087.16	10820.65
114_mis_A_T	265.82	580.90	835.92
115_mis_T_A	622.57	3369.54	1710.74
115_mis_T_C	146.90	551.51	1714.43
115_mis_T_G	1105.24	1273.30	1161.93
116_mis_A_C	496.66	701.05	670.04
116_mis_A_G	1951.66	3212.22	4949.57
116_mis_A_T	328.77	108.05	834.69
117_mis_G_A	111.92	4580.61	2674.45
117_mis_G_C	181.88	172.02	122.46
117_mis_G_T	8457.21	3570.96	1426.10
118_mis_C_A	8170.40	5286.85	3013.15
118_mis_C_G	384.74	1163.52	1486.30
118_mis_C_T	923.37	2320.13	5377.56
119_mis_G_A	965.34	5861.69	2574.51
119_mis_G_C	41.97	298.23	92.97
119_mis_G_T	6995.21	2280.36	1021.86
120_mis_A_C	328.77	223.89	376.80
120_mis_A_G	223.85	2684.92	4576.45
120_mis_A_T	76.95	163.38	98.30
121_mis_A_C	636.56	578.30	813.39
121_mis_A_G	461.68	5668.06	10273.06
121_mis_A_T	0.00	101.14	334.61
122_mis_G_A	1650.87	4317.82	3555.41
122_mis_G_C	34.98	54.46	39.73
122_mis_G_T	538.63	95.95	394.82
123_mis_A_C	251.83	64.83	292.84
123_mis_A_G	727.50	4782.89	9592.78
123_mis_A_T	20.99	82.12	48.33
124_mis_G_A	258.82	4400.81	2735.06
124_mis_G_C	0.00	32.85	23.75
124_mis_G_T	4945.61	1502.38	1192.24
125_mis_G_A	1154.21	5393.17	2280.45
125_mis_G_C	62.96	90.77	63.07
125_mis_G_T	17278.16	3435.24	2522.50
126_mis_C_A	17865.76	4601.36	2532.74
126_mis_C_G	559.62	2473.13	2583.93
126_mis_C_T	3238.78	2706.53	5546.71
127_mis_C_A	7477.88	3668.64	2251.37
127_mis_C_G	363.75	625.85	455.02
127_mis_C_T	2252.46	763.29	1286.44
128_mis_C_A	10730.65	7060.66	3560.74
128_mis_C_G	1084.26	806.51	908.00
128_mis_C_T	2462.31	1153.15	1603.03
129_mis_G_A	7526.84	8868.18	3899.04
129_mis_G_C	244.83	186.72	124.51
129_mis_G_T	10702.67	2684.05	1831.56
130_mis_C_A	8716.03	7393.46	4492.08
130_mis_C_G	538.63	776.26	1559.21
130_mis_C_T	216.85	2717.76	4733.73
131_mis_A_C	2056.59	2397.06	2403.31
131_mis_A_G	1266.13	2247.52	3128.65
131_mis_A_T	496.66	251.55	606.15
132_mis_C_A	4211.12	1789.37	1988.02
132_mis_C_G	55.96	722.66	1301.59
132_mis_C_T	986.32	4287.57	6871.24
133_mis_C_A	8988.84	3471.55	2410.28
133_mis_C_G	237.84	184.12	442.33
133_mis_C_T	1301.11	1311.34	2213.28
134_mis_G_A	1622.89	6308.60	2235.80
134_mis_G_C	118.92	77.80	101.98
134_mis_G_T	3693.47	1090.05	430.86
135_mis_A_C	685.53	387.26	657.35
135_mis_A_G	643.56	2096.24	3960.47
135_mis_A_T	132.91	555.83	187.58
136_mis_T_A	139.90	729.58	1113.19
136_mis_T_C	461.68	663.02	849.84
136_mis_T_G	482.67	429.62	371.88
137_mis_C_A	3931.31	3688.52	1848.77
137_mis_C_G	363.75	348.36	450.52
137_mis_C_T	615.58	1060.65	2309.52
138_mis_G_A	1224.16	3611.58	2456.97
138_mis_G_C	160.89	246.36	257.21
138_mis_G_T	11038.44	2961.53	1442.89
139_mis_C_A	5225.42	3228.64	1972.04
139_mis_C_G	251.83	663.88	1086.98
139_mis_C_T	503.65	3421.41	6168.83
140_mis_C_A	3000.94	2210.34	2582.70
140_mis_C_G	790.46	587.81	686.43
140_mis_C_T	692.53	1238.73	2043.31
141_mis_C_A	6421.60	3441.29	2064.20
141_mis_C_G	181.88	389.86	138.43
141_mis_C_T	720.51	1234.40	2287.00
142_mis_T_A	510.65	245.50	751.96
142_mis_T_C	503.65	843.68	728.20
142_mis_T_G	2056.59	1562.89	1290.12
143_mis_T_A	356.76	1280.22	954.28
143_mis_T_C	405.72	321.57	505.40
143_mis_T_G	2364.38	2496.47	2334.51
144_mis_C_A	4169.14	3729.15	1941.33
144_mis_C_G	216.85	329.35	501.30
144_mis_C_T	587.60	1195.51	3499.30
145_mis_C_A	5323.35	4082.70	1801.67
145_mis_C_G	293.80	216.97	267.44
145_mis_C_T	90.94	1386.54	2372.19
146_mis_C_A	10240.98	5374.16	3995.69
146_mis_C_G	20.99	54.46	239.18
146_mis_C_T	664.54	598.18	1341.32
147_mis_A_C	188.87	115.83	149.49
147_mis_A_G	293.80	907.65	1401.52
147_mis_A_T	0.00	112.38	655.30
148_mis_A_C	265.82	300.82	290.79
148_mis_A_G	363.75	2289.01	4244.30
148_mis_A_T	188.87	217.84	218.30
149_mis_C_A	3371.69	3693.71	2592.94
149_mis_C_G	251.83	126.21	187.99
149_mis_C_T	1238.15	3671.23	6352.73
150_mis_A_C	517.65	367.38	743.36
150_mis_A_G	384.74	2040.92	2382.84
150_mis_A_T	174.88	486.67	384.58
151_mis_G_A	328.77	5515.06	2621.20
151_mis_G_C	20.99	51.00	19.25
151_mis_G_T	7939.56	2088.46	1290.94
152_mis_T_A	216.85	2290.74	1684.94
152_mis_T_C	419.71	516.93	792.50
152_mis_T_G	734.50	637.95	992.78
153_mis_T_A	62.96	976.80	923.56
153_mis_T_C	916.37	344.04	532.43
153_mis_T_G	2112.55	2026.22	2024.47
154_mis_G_A	664.54	4650.63	2395.53
154_mis_G_C	55.96	51.00	73.31
154_mis_G_T	6904.27	1637.23	798.65
155_mis_C_A	5799.03	3900.30	2645.78
155_mis_C_G	384.74	1123.76	1335.99
155_mis_C_T	2504.28	3529.46	4355.70
156_mis_G_A	2770.10	6883.45	3366.61
156_mis_G_C	62.96	146.95	133.11
156_mis_G_T	9065.79	1765.16	1806.58
157_mis_C_A	7785.67	6208.33	3121.69
157_mis_C_G	167.88	1053.74	1797.57
157_mis_C_T	594.59	1223.17	5555.31
158_mis_A_C	398.73	455.55	692.16
158_mis_A_G	1371.06	2730.73	3072.54
158_mis_A_T	510.65	817.75	842.88
159_mis_G_A	174.88	4408.59	2477.45
159_mis_G_C	27.98	69.15	77.82
159_mis_G_T	9072.79	2003.75	2199.35
160_mis_C_A	5267.39	3730.01	2877.18
160_mis_C_G	475.67	686.36	1366.30
160_mis_C_T	888.39	2410.89	6447.75
161_mis_C_A	5421.29	2298.52	2221.06
161_mis_C_G	83.94	73.48	205.60
161_mis_C_T	426.71	1504.97	2133.00
162_mis_T_A	594.59	1769.49	1167.66
162_mis_T_C	3455.63	1262.93	733.12
162_mis_T_G	1916.69	1164.39	907.59
163_mis_G_A	538.63	5462.33	2514.31
163_mis_G_C	0.00	82.12	109.76
163_mis_G_T	6400.62	2614.90	1102.95
164_mis_A_C	0.00	126.21	444.38
164_mis_A_G	209.86	2278.63	4613.72
164_mis_A_T	223.85	143.50	267.03
165_mis_A_C	76.95	290.45	439.46
165_mis_A_G	279.81	4185.57	11062.29
165_mis_A_T	27.98	328.48	185.12
166_mis_T_A	412.72	2378.91	1260.22
166_mis_T_C	314.78	642.27	843.70
166_mis_T_G	1748.80	1663.16	1614.91
167_mis_G_A	1133.22	4545.17	2965.64
167_mis_G_C	0.00	62.24	88.06
167_mis_G_T	8233.36	1806.66	918.24
168_mis_G_A	1224.16	5907.51	3236.77
168_mis_G_C	62.96	31.12	111.40
168_mis_G_T	9205.69	2323.59	1297.09
169_mis_C_A	6722.40	4919.47	2214.10
169_mis_C_G	433.70	647.46	545.13
169_mis_C_T	1615.89	2328.77	5051.55
170_mis_G_A	706.52	6000.87	3130.70
170_mis_G_C	552.62	46.68	87.65
170_mis_G_T	4106.19	1557.70	894.08
171_mis_A_C	783.46	670.80	680.28
171_mis_A_G	230.84	3079.10	4621.10
171_mis_A_T	174.88	247.23	242.87
172_mis_A_C	76.95	280.94	1231.56
172_mis_A_G	377.74	6774.53	13171.54
172_mis_A_T	167.88	245.50	480.83
173_mis_T_A	391.73	2824.09	980.08
173_mis_T_C	20.99	907.65	1339.68
173_mis_T_G	587.60	657.83	792.91
174_mis_G_A	356.76	5760.55	3172.47
174_mis_G_C	0.00	63.10	88.88
174_mis_G_T	6260.71	1447.92	869.50
175_mis_G_A	972.33	5941.22	3302.71
175_mis_G_C	139.90	52.73	28.67
175_mis_G_T	9254.66	4141.48	1764.40
176_mis_C_A	10394.88	5501.23	2995.54
176_mis_C_G	587.60	841.95	1505.14
176_mis_C_T	4448.95	2477.45	4424.10
177_mis_G_A	1441.01	6838.50	2333.69
177_mis_G_C	104.93	354.42	34.40
177_mis_G_T	10436.85	2891.51	1232.78
178_mis_C_A	5917.95	3136.15	2184.20
178_mis_C_G	181.88	279.21	674.55
178_mis_C_T	160.89	4110.36	5624.94
179_mis_T_A	321.78	284.40	394.00
179_mis_T_C	209.86	391.59	226.90
179_mis_T_G	706.52	921.48	717.55
180_mis_A_C	202.86	194.50	487.79
180_mis_A_G	195.87	361.33	882.20
180_mis_A_T	125.91	125.34	280.55
181_mis_A_C	384.74	336.26	328.47
181_mis_A_G	48.97	660.42	2409.05
181_mis_A_T	55.96	135.72	249.01
182_mis_T_A	265.82	251.55	315.36
182_mis_T_C	55.96	297.36	530.79
182_mis_T_G	419.71	380.35	363.28
183_mis_A_C	398.73	212.65	384.17
183_mis_A_G	230.84	370.84	619.67
183_mis_A_T	69.95	60.51	135.16
184_mis_A_C	104.93	396.77	460.76
184_mis_A_G	111.92	278.35	1363.43
184_mis_A_T	132.91	104.60	101.16
185_mis_G_A	370.75	372.57	1285.21
185_mis_G_C	132.91	83.85	38.50
185_mis_G_T	552.62	335.40	581.58
186_mis_A_C	244.83	172.89	383.76
186_mis_A_G	230.84	499.64	1874.98
186_mis_A_T	195.87	160.78	286.28
187_mis_T_A	251.83	399.37	495.57
187_mis_T_C	174.88	242.90	571.75
187_mis_T_G	615.58	416.65	399.73
188_mis_A_C	510.65	318.97	387.45
188_mis_A_G	181.88	427.89	1674.29
188_mis_A_T	216.85	114.97	271.95
189_mis_T_A	258.82	311.19	514.41
189_mis_T_C	139.90	220.43	266.22
189_mis_T_G	419.71	519.52	351.00
190_mis_C_A	363.75	787.49	821.17
190_mis_C_G	0.00	42.36	81.91
190_mis_C_T	195.87	82.99	337.07
191_mis_A_C	272.81	395.91	383.76
191_mis_A_G	363.75	197.09	695.44
191_mis_A_T	118.92	244.63	194.54
192_mis_T_A	160.89	241.18	334.61
192_mis_T_C	230.84	390.72	382.94
192_mis_T_G	811.44	478.03	568.06
193_mis_C_A	209.86	616.34	417.75
193_mis_C_G	27.98	95.09	72.49
193_mis_C_T	0.00	306.01	680.28
194_mis_G_A	146.90	453.83	549.22
194_mis_G_C	90.94	76.07	65.94
194_mis_G_T	125.91	161.65	124.51
195_mis_G_A	405.72	1197.23	959.61
195_mis_G_C	216.85	172.89	88.06
195_mis_G_T	657.55	663.02	833.05
196_mis_C_A	41.97	370.84	578.71
196_mis_C_G	237.84	255.87	477.14
196_mis_C_T	153.89	582.63	2262.02
197_mis_T_A	125.91	64.83	226.08
197_mis_T_C	97.93	124.48	137.20
197_mis_T_G	314.78	344.91	244.10
198_mis_T_A	97.93	170.29	343.21
198_mis_T_C	293.80	191.90	578.30
198_mis_T_G	1210.17	870.48	1225.82
199_mis_T_A	34.98	550.64	579.53
199_mis_T_C	370.75	537.67	704.04
199_mis_T_G	454.69	335.40	455.84

## Normalized table: miss_indexes_by_string.

	s1	s2	s3
024_mis_C_A	5626.0	4224.47	2388.55
024_mis_C_G	0.0	787.87	1124.93
024_mis_C_T	1433.4	1470.69	4465.04
025_mis_C_A	5948.5	5064.87	2619.70
025_mis_C_G	286.7	780.36	473.86
025_mis_C_T	1612.6	2468.65	1906.99
026_mis_G_A	1433.4	10617.46	8340.65
026_mis_G_C	788.4	1298.11	1356.08
026_mis_G_T	8851.1	2648.74	1594.93
027_mis_T_A	0.0	697.83	1236.65
027_mis_T_C	3511.8	1733.31	1783.71
027_mis_T_G	322.5	1988.43	1910.84
028_mis_C_A	2508.4	3999.37	2111.17
028_mis_C_G	107.5	247.62	404.51
028_mis_C_T	1540.9	1635.76	4214.63
029_mis_G_A	788.4	8854.14	5250.95
029_mis_G_C	860.0	472.72	408.36
029_mis_G_T	10392.0	1838.36	1548.70
030_mis_T_A	107.5	67.53	250.41
030_mis_T_C	1146.7	1343.13	1467.80
030_mis_T_G	9890.3	5860.24	5397.35
031_mis_T_A	0.0	255.12	481.56
031_mis_T_C	322.5	480.22	720.42
031_mis_T_G	501.7	105.05	134.84
032_mis_T_A	0.0	135.06	77.05
032_mis_T_C	788.4	322.65	570.17
032_mis_T_G	179.2	75.04	42.38
033_mis_T_A	358.3	195.09	1117.22
033_mis_T_C	680.9	682.82	739.68
033_mis_T_G	0.0	52.52	104.02
034_mis_A_C	2365.1	997.97	893.78
034_mis_A_G	2221.7	2536.19	5123.82
034_mis_A_T	2257.6	2453.65	1660.43
035_mis_C_A	3583.5	3204.00	2068.79
035_mis_C_G	0.0	0.00	269.67
035_mis_C_T	1003.4	4314.52	8086.39
036_mis_A_C	1505.1	4584.64	5817.27
036_mis_A_G	967.5	2348.60	2457.89
036_mis_A_T	0.0	337.66	454.59
037_mis_A_C	4479.3	2521.18	2134.28
037_mis_A_G	3511.8	3001.40	6387.44
037_mis_A_T	0.0	315.15	285.08
038_mis_C_A	4658.5	3864.31	3058.88
038_mis_C_G	250.8	165.08	323.61
038_mis_C_T	1182.5	2626.23	4746.27
039_mis_G_A	1791.7	7375.95	3894.87
039_mis_G_C	752.5	2918.86	2870.11
039_mis_G_T	7095.2	2408.63	1914.69
040_mis_T_A	107.5	157.57	550.91
040_mis_T_C	2830.9	1643.27	1533.29
040_mis_T_G	215.0	2311.08	1914.69
041_mis_C_A	5912.7	2821.32	2831.58
041_mis_C_G	143.3	90.04	639.51
041_mis_C_T	322.5	877.91	2199.78
042_mis_G_A	1612.6	6633.10	3517.33
042_mis_G_C	394.2	1118.02	1483.21
042_mis_G_T	6916.1	1950.91	943.86
043_mis_T_A	143.3	525.25	824.43
043_mis_T_C	394.2	960.45	816.73
043_mis_T_G	3225.1	3856.80	3563.56
044_mis_G_A	645.0	4974.83	3798.56
044_mis_G_C	0.0	112.55	177.21
044_mis_G_T	11717.9	3219.00	1991.74
045_mis_A_C	3870.1	2003.44	2068.79
045_mis_A_G	250.8	3391.59	9519.52
045_mis_A_T	215.0	487.73	273.53
046_mis_C_A	2185.9	4254.49	2246.01
046_mis_C_G	0.0	997.97	1460.10
046_mis_C_T	860.0	5289.97	12512.91
047_mis_T_A	430.0	2363.61	1537.15
047_mis_T_C	1648.4	4134.43	4391.85
047_mis_T_G	4156.8	1290.60	1190.42
048_mis_G_A	860.0	6453.02	4938.90
048_mis_G_C	0.0	60.03	34.67
048_mis_G_T	7668.6	2558.70	1552.56
049_mis_G_A	1075.0	10069.71	5320.30
049_mis_G_C	573.4	307.64	181.07
049_mis_G_T	8528.6	2131.00	1664.28
050_mis_G_A	2615.9	10062.20	18857.97
050_mis_G_C	286.7	262.62	150.25
050_mis_G_T	3977.6	697.83	728.12
051_mis_A_C	358.3	412.69	412.22
051_mis_A_G	4013.5	8869.15	11276.25
051_mis_A_T	179.2	195.09	169.51
052_mis_A_C	394.2	345.16	566.32
052_mis_A_G	179.2	4847.27	10763.87
052_mis_A_T	0.0	217.60	211.89
053_mis_A_C	680.9	510.24	920.75
053_mis_A_G	179.2	6295.44	10879.45
053_mis_A_T	0.0	75.04	481.56
054_mis_A_C	18024.8	6070.34	2650.52
054_mis_A_G	143.3	5357.50	8317.54
054_mis_A_T	0.0	0.00	327.46
055_mis_C_A	5805.2	8996.71	6206.37
055_mis_C_G	0.0	630.29	416.07
055_mis_C_T	1110.9	1643.27	4522.83
056_mis_C_A	8779.5	3766.76	2623.55
056_mis_C_G	501.7	247.62	392.95
056_mis_C_T	322.5	1515.71	2045.68
057_mis_C_A	9782.8	5605.12	3105.11
057_mis_C_G	0.0	187.59	354.43
057_mis_C_T	11646.2	3286.54	1776.00
058_mis_T_A	215.0	1583.24	1186.57
058_mis_T_C	4873.5	5214.94	3813.97
058_mis_T_G	824.2	442.71	431.48
059_mis_G_A	7847.8	7158.35	3648.31
059_mis_G_C	250.8	300.14	204.18
059_mis_G_T	10607.0	3534.15	2592.73
060_mis_G_A	179.2	5792.71	2534.94
060_mis_G_C	2221.7	1313.11	1082.55
060_mis_G_T	22826.6	4464.59	2951.01
061_mis_C_A	8277.8	4937.31	2442.48
061_mis_C_G	501.7	1042.99	1413.87
061_mis_C_T	322.5	2521.18	6549.24
062_mis_G_A	1433.4	7053.30	3255.36
062_mis_G_C	0.0	780.36	820.58
062_mis_G_T	7489.4	2183.52	1425.42
063_mis_T_A	0.0	285.13	600.99
063_mis_T_C	322.5	645.30	905.34
063_mis_T_G	931.7	5237.45	4515.12
064_mis_T_A	286.7	1320.62	855.25
064_mis_T_C	537.5	855.40	936.16
064_mis_T_G	0.0	22.51	127.13
065_mis_A_C	3691.0	1635.76	1660.43
065_mis_A_G	143.3	3834.29	7362.12
065_mis_A_T	1290.0	2633.73	2866.26
066_mis_C_A	967.5	2986.40	2138.14
066_mis_C_G	0.0	540.25	1101.81
066_mis_C_T	1612.6	7105.82	14839.81
067_mis_C_A	2472.6	3466.62	2126.58
067_mis_C_G	0.0	352.66	208.03
067_mis_C_T	1755.9	2423.63	2873.96
068_mis_C_A	9137.8	4487.10	2885.52
068_mis_C_G	0.0	315.15	458.45
068_mis_C_T	1540.9	1080.51	1379.19
069_mis_A_C	430.0	630.29	362.13
069_mis_A_G	716.7	967.95	1151.90
069_mis_A_T	0.0	817.88	666.48
070_mis_A_C	680.9	255.12	489.27
070_mis_A_G	501.7	3053.93	5747.92
070_mis_A_T	107.5	300.14	277.38
071_mis_C_A	2723.4	2085.98	1633.46
071_mis_C_G	0.0	592.78	778.20
071_mis_C_T	1003.4	3339.06	6476.05
072_mis_T_A	0.0	142.57	354.43
072_mis_T_C	215.0	232.61	647.22
072_mis_T_G	286.7	60.03	77.05
073_mis_T_A	0.0	600.28	323.61
073_mis_T_C	179.2	330.15	431.48
073_mis_T_G	0.0	75.04	146.39
074_mis_A_C	107.5	720.34	335.17
074_mis_A_G	143.3	2423.63	4045.12
074_mis_A_T	250.8	382.68	681.89
075_mis_A_C	0.0	465.22	708.86
075_mis_A_G	0.0	3999.37	7778.19
075_mis_A_T	0.0	465.22	261.97
076_mis_T_A	430.0	2138.50	1232.80
076_mis_T_C	250.8	840.39	1402.31
076_mis_T_G	0.0	97.55	154.10
077_mis_C_A	6235.2	4637.17	3305.44
077_mis_C_G	0.0	300.14	396.81
077_mis_C_T	1397.5	1185.55	3020.36
078_mis_G_A	609.2	5132.40	2985.68
078_mis_G_C	143.3	97.55	177.21
078_mis_G_T	16268.9	3249.02	2430.92
079_mis_C_A	8134.5	3196.49	1525.59
079_mis_C_G	0.0	435.20	940.01
079_mis_C_T	430.0	2401.12	4908.08
080_mis_C_A	3870.1	2033.45	1444.69
080_mis_C_G	143.3	30.01	111.72
080_mis_C_T	680.9	1710.80	2750.68
081_mis_T_A	179.2	412.69	735.83
081_mis_T_C	394.2	300.14	581.73
081_mis_T_G	0.0	127.56	231.15
082_mis_T_A	0.0	990.46	1159.60
082_mis_T_C	143.3	660.31	639.51
082_mis_T_G	0.0	97.55	80.90
083_mis_G_A	537.5	4652.17	2500.27
083_mis_G_C	322.5	120.06	88.61
083_mis_G_T	12542.1	2258.56	1729.77
084_mis_C_A	7166.9	2281.07	1552.56
084_mis_C_G	0.0	202.59	392.95
084_mis_C_T	1218.4	3781.77	7631.79
085_mis_A_C	0.0	210.10	392.95
085_mis_A_G	895.9	1185.55	2219.04
085_mis_A_T	0.0	622.79	392.95
086_mis_G_A	4300.2	6700.63	3756.18
086_mis_G_C	430.0	165.08	227.30
086_mis_G_T	8672.0	2063.46	1379.19
087_mis_C_A	9030.3	5800.21	3182.16
087_mis_C_G	107.5	1350.63	1483.21
087_mis_C_T	573.4	1695.79	6861.29
088_mis_A_C	322.5	472.72	454.59
088_mis_A_G	394.2	1703.30	2238.30
088_mis_A_T	250.8	337.66	481.56
089_mis_C_A	1540.9	3646.70	2527.24
089_mis_C_G	0.0	817.88	658.78
089_mis_C_T	1146.7	4614.66	6452.93
090_mis_A_C	179.2	607.78	924.60
090_mis_A_G	286.7	1748.32	3840.94
090_mis_A_T	143.3	195.09	758.94
091_mis_T_A	0.0	2341.09	1213.54
091_mis_T_C	573.4	675.32	1101.81
091_mis_T_G	0.0	52.52	77.05
092_mis_C_A	4730.2	2513.68	1386.90
092_mis_C_G	0.0	442.71	319.76
092_mis_C_T	1110.9	1455.68	2461.74
093_mis_C_A	5769.4	4907.29	4137.58
093_mis_C_G	250.8	832.89	454.59
093_mis_C_T	716.7	1283.10	1564.11
094_mis_C_A	10033.7	7083.31	2430.92
094_mis_C_G	107.5	225.11	443.04
094_mis_C_T	501.7	877.91	1914.69
095_mis_C_A	10535.4	5522.58	2592.73
095_mis_C_G	0.0	262.62	373.69
095_mis_C_T	501.7	660.31	916.89
096_mis_C_A	8887.0	5079.87	2149.69
096_mis_C_G	0.0	127.56	154.10
096_mis_C_T	1075.0	1718.30	2323.05
097_mis_T_A	0.0	915.43	1101.81
097_mis_T_C	501.7	645.30	169.51
097_mis_T_G	0.0	247.62	100.16
098_mis_T_A	215.0	937.94	847.55
098_mis_T_C	179.2	495.23	535.50
098_mis_T_G	179.2	45.02	77.05
099_mis_T_A	0.0	112.55	127.13
099_mis_T_C	430.0	585.27	377.54
099_mis_T_G	0.0	37.52	46.23
100_mis_C_A	6414.4	3414.10	1648.87
100_mis_C_G	107.5	37.52	42.38
100_mis_C_T	1827.6	16860.38	12501.35
101_mis_G_A	1433.4	4817.25	2727.57
101_mis_G_C	573.4	180.08	169.51
101_mis_G_T	8349.5	2498.67	1248.21
102_mis_C_A	8421.1	2506.17	1213.54
102_mis_C_G	0.0	90.04	84.75
102_mis_C_T	1827.6	1928.40	4079.79
103_mis_C_A	4049.3	2701.26	1190.42
103_mis_C_G	0.0	105.05	146.39
103_mis_C_T	1290.0	1185.55	1614.20
104_mis_A_C	143.3	390.18	196.48
104_mis_A_G	286.7	720.34	1348.37
104_mis_A_T	179.2	555.26	654.92
105_mis_G_A	609.2	4614.66	3193.72
105_mis_G_C	143.3	0.00	23.11
105_mis_G_T	12291.3	3083.94	2261.41
106_mis_C_A	5339.4	5034.85	2843.14
106_mis_C_G	0.0	487.73	928.45
106_mis_C_T	1505.1	2153.51	5428.17
107_mis_T_A	0.0	2183.52	1244.36
107_mis_T_C	394.2	240.11	315.90
107_mis_T_G	322.5	480.22	543.20
108_mis_G_A	537.5	4292.01	2080.35
108_mis_G_C	215.0	165.08	38.52
108_mis_G_T	7310.3	1838.36	1009.35
109_mis_G_A	465.8	3504.14	2816.17
109_mis_G_C	0.0	150.07	53.93
109_mis_G_T	9281.2	3143.97	1791.41
110_mis_C_A	7991.1	4914.80	2446.33
110_mis_C_G	1469.2	735.34	770.50
110_mis_C_T	3476.0	3294.04	7712.70
111_mis_G_A	5267.7	6588.08	2816.17
111_mis_G_C	0.0	142.57	96.31
111_mis_G_T	10965.4	2326.09	1363.78
112_mis_T_A	250.8	1027.98	970.83
112_mis_T_C	1755.9	870.41	839.84
112_mis_T_G	2938.4	3083.94	2977.98
113_mis_A_C	0.0	127.56	416.07
113_mis_A_G	250.8	3023.91	5331.85
113_mis_A_T	0.0	562.76	681.89
114_mis_A_C	107.5	592.78	1040.17
114_mis_A_G	215.0	5139.90	10440.26
114_mis_A_T	215.0	622.79	812.88
115_mis_T_A	716.7	3354.07	1841.49
115_mis_T_C	215.0	705.33	1583.38
115_mis_T_G	1325.9	1403.16	1448.54
116_mis_A_C	609.2	727.84	797.47
116_mis_A_G	2042.6	3158.98	4842.59
116_mis_A_T	286.7	127.56	654.92
117_mis_G_A	143.3	4697.20	2608.14
117_mis_G_C	143.3	187.59	107.87
117_mis_G_T	8779.5	3143.97	1544.85
118_mis_C_A	8026.9	5184.92	2754.53
118_mis_C_G	394.2	1208.06	1533.29
118_mis_C_T	1003.4	2333.59	5281.77
119_mis_G_A	967.5	5627.63	2450.19
119_mis_G_C	0.0	270.13	119.43
119_mis_G_T	7274.4	2356.10	1024.76
120_mis_A_C	358.3	285.13	454.59
120_mis_A_G	250.8	2851.33	4403.40
120_mis_A_T	107.5	172.58	146.39
121_mis_A_C	501.7	510.24	658.78
121_mis_A_G	537.5	5620.13	10043.46
121_mis_A_T	0.0	135.06	339.02
122_mis_G_A	1182.5	4081.91	3397.90
122_mis_G_C	0.0	67.53	53.93
122_mis_G_T	430.0	135.06	431.48
123_mis_A_C	215.0	75.04	315.90
123_mis_A_G	931.7	4367.04	9014.84
123_mis_A_T	0.0	120.06	80.90
124_mis_G_A	394.2	4569.64	2611.99
124_mis_G_C	0.0	52.52	38.52
124_mis_G_T	5446.9	1620.76	1348.37
125_mis_G_A	1325.9	5064.87	2269.12
125_mis_G_C	107.5	127.56	80.90
125_mis_G_T	16913.9	3729.24	2581.17
126_mis_C_A	15516.4	4539.62	2608.14
126_mis_C_G	609.2	2453.65	2577.32
126_mis_C_T	3045.9	2768.79	5146.93
127_mis_C_A	7632.8	3549.16	2253.71
127_mis_C_G	430.0	562.76	504.68
127_mis_C_T	2150.1	847.90	1317.55
128_mis_C_A	10571.2	6543.06	3274.62
128_mis_C_G	1003.4	907.92	1105.67
128_mis_C_T	2078.4	1253.09	1398.46
129_mis_G_A	7704.4	7683.59	3891.02
129_mis_G_C	322.5	202.59	161.80
129_mis_G_T	11144.6	2596.21	1714.36
130_mis_C_A	8600.3	7038.29	4045.12
130_mis_C_G	537.5	885.41	1552.56
130_mis_C_T	322.5	2626.23	4569.06
131_mis_A_C	2329.2	2828.82	2916.34
131_mis_A_G	1218.4	2258.56	3166.75
131_mis_A_T	430.0	255.12	566.32
132_mis_C_A	3906.0	1710.80	1976.33
132_mis_C_G	0.0	765.36	1236.65
132_mis_C_T	1182.5	3556.66	6564.65
133_mis_C_A	7166.9	3504.14	2269.12
133_mis_C_G	286.7	195.09	523.94
133_mis_C_T	1684.2	1373.14	2180.51
134_mis_G_A	1433.4	6483.03	2249.86
134_mis_G_C	107.5	90.04	127.13
134_mis_G_T	3547.6	1118.02	458.45
135_mis_A_C	716.7	465.22	697.30
135_mis_A_G	680.9	1935.90	3871.76
135_mis_A_T	179.2	592.78	231.15
136_mis_T_A	143.3	750.35	1163.45
136_mis_T_C	573.4	735.34	966.98
136_mis_T_G	537.5	495.23	458.45
137_mis_C_A	3619.3	3586.68	1876.17
137_mis_C_G	394.2	345.16	516.23
137_mis_C_T	680.9	1027.98	2034.12
138_mis_G_A	1290.0	3706.73	2585.02
138_mis_G_C	179.2	292.64	277.38
138_mis_G_T	10786.2	3016.41	1483.21
139_mis_C_A	4801.8	2948.88	2168.95
139_mis_C_G	250.8	727.84	1128.78
139_mis_C_T	573.4	3196.49	5990.63
140_mis_C_A	2687.6	2206.03	2319.20
140_mis_C_G	788.4	525.25	647.22
140_mis_C_T	967.5	1403.16	2049.53
141_mis_C_A	6199.4	3249.02	1960.92
141_mis_C_G	179.2	307.64	157.95
141_mis_C_T	860.0	1358.13	2107.32
142_mis_T_A	465.8	322.65	843.70
142_mis_T_C	501.7	870.41	801.32
142_mis_T_G	2078.4	1823.35	1583.38
143_mis_T_A	322.5	1350.63	978.53
143_mis_T_C	537.5	405.19	624.10
143_mis_T_G	2436.8	2933.87	2816.17
144_mis_C_A	4622.7	3504.14	1872.31
144_mis_C_G	215.0	307.64	535.50
144_mis_C_T	752.5	1305.61	3343.97
145_mis_C_A	4909.3	3661.71	2076.50
145_mis_C_G	322.5	277.63	254.26
145_mis_C_T	143.3	1253.09	2111.17
146_mis_C_A	8600.3	5162.41	4237.75
146_mis_C_G	0.0	67.53	196.48
146_mis_C_T	860.0	615.29	1298.29
147_mis_A_C	179.2	142.57	188.77
147_mis_A_G	322.5	937.94	1417.72
147_mis_A_T	0.0	165.08	543.20
148_mis_A_C	286.7	337.66	346.72
148_mis_A_G	537.5	2243.55	4133.73
148_mis_A_T	215.0	210.10	265.82
149_mis_C_A	3655.1	3811.78	2577.32
149_mis_C_G	250.8	180.08	254.26
149_mis_C_T	824.2	3541.66	5955.96
150_mis_A_C	501.7	412.69	862.96
150_mis_A_G	358.3	1793.34	2523.38
150_mis_A_T	179.2	405.19	381.40
151_mis_G_A	286.7	5500.07	2538.79
151_mis_G_C	0.0	60.03	26.97
151_mis_G_T	8206.1	1950.91	1190.42
152_mis_T_A	250.8	2273.56	1567.97
152_mis_T_C	394.2	637.80	778.20
152_mis_T_G	716.7	780.36	1059.44
153_mis_T_A	107.5	990.46	940.01
153_mis_T_C	1003.4	367.67	643.37
153_mis_T_G	2257.6	2491.16	2496.42
154_mis_G_A	645.0	4427.07	2207.48
154_mis_G_C	0.0	60.03	88.61
154_mis_G_T	7417.8	1620.76	897.63
155_mis_C_A	6163.5	3744.25	2515.68
155_mis_C_G	465.8	1163.04	1344.52
155_mis_C_T	3081.8	3511.64	4418.81
156_mis_G_A	2544.3	6520.55	3455.69
156_mis_G_C	0.0	150.07	173.36
156_mis_G_T	9317.0	2153.51	1664.28
157_mis_C_A	7131.1	6377.98	3078.14
157_mis_C_G	143.3	1163.04	1760.59
157_mis_C_T	752.5	1493.20	4915.78
158_mis_A_C	394.2	540.25	681.89
158_mis_A_G	1290.0	2873.84	3251.51
158_mis_A_T	465.8	780.36	801.32
159_mis_G_A	250.8	4689.69	2754.53
159_mis_G_C	0.0	90.04	107.87
159_mis_G_T	9424.5	2326.09	2353.87
160_mis_C_A	5482.7	4036.89	2492.56
160_mis_C_G	430.0	795.37	1363.78
160_mis_C_T	1218.4	2461.15	6464.49
161_mis_C_A	5124.3	2416.13	2138.14
161_mis_C_G	0.0	97.55	231.15
161_mis_C_T	645.0	1343.13	2053.38
162_mis_T_A	680.9	1815.85	1225.09
162_mis_T_C	3296.8	1440.67	828.29
162_mis_T_G	1863.4	1380.65	1121.08
163_mis_G_A	501.7	5184.92	2585.02
163_mis_G_C	0.0	82.54	111.72
163_mis_G_T	5876.9	2318.58	1067.14
164_mis_A_C	0.0	127.56	446.89
164_mis_A_G	286.7	2416.13	4349.47
164_mis_A_T	250.8	142.57	331.31
165_mis_A_C	0.0	277.63	504.68
165_mis_A_G	358.3	4231.98	10798.55
165_mis_A_T	0.0	375.18	238.85
166_mis_T_A	501.7	2806.31	1506.33
166_mis_T_C	465.8	727.84	820.58
166_mis_T_G	2042.6	1890.88	1883.87
167_mis_G_A	1325.9	4659.68	3178.31
167_mis_G_C	0.0	75.04	88.61
167_mis_G_T	8636.1	2003.44	955.42
168_mis_G_A	1755.9	5792.71	3447.98
168_mis_G_C	107.5	30.01	127.13
168_mis_G_T	9424.5	2416.13	1352.23
169_mis_C_A	6880.2	4667.18	2461.74
169_mis_C_G	501.7	720.34	670.33
169_mis_C_T	1684.2	2258.56	5019.80
170_mis_G_A	752.5	6190.39	3055.03
170_mis_G_C	537.5	52.52	100.16
170_mis_G_T	4371.8	1590.74	970.83
171_mis_A_C	824.2	772.86	793.61
171_mis_A_G	286.7	3001.40	4784.80
171_mis_A_T	215.0	240.11	281.23
172_mis_A_C	0.0	352.66	1078.70
172_mis_A_G	358.3	6618.09	13032.99
172_mis_A_T	250.8	277.63	466.15
173_mis_T_A	465.8	2791.30	1090.26
173_mis_T_C	0.0	855.40	1148.04
173_mis_T_G	573.4	877.91	966.98
174_mis_G_A	394.2	5267.46	3035.77
174_mis_G_C	0.0	60.03	111.72
174_mis_G_T	4945.2	1538.22	905.34
175_mis_G_A	1110.9	5942.78	3132.08
175_mis_G_C	143.3	60.03	42.38
175_mis_G_T	9854.5	4382.05	1887.72
176_mis_C_A	8958.6	5755.19	3004.95
176_mis_C_G	645.0	892.92	1529.44
176_mis_C_T	4801.8	2738.78	4861.85
177_mis_G_A	1469.2	6400.49	2457.89
177_mis_G_C	179.2	277.63	46.23
177_mis_G_T	10105.4	2843.83	1298.29
178_mis_C_A	6056.0	3106.45	2280.68
178_mis_C_G	179.2	405.19	762.79
178_mis_C_T	179.2	3826.79	5636.20
179_mis_T_A	358.3	375.18	466.15
179_mis_T_C	286.7	532.75	331.31
179_mis_T_G	680.9	1005.47	878.37
180_mis_A_C	215.0	292.64	470.00
180_mis_A_G	179.2	412.69	928.45
180_mis_A_T	107.5	187.59	269.67
181_mis_A_C	394.2	367.67	412.22
181_mis_A_G	0.0	607.78	2396.25
181_mis_A_T	0.0	210.10	296.64
182_mis_T_A	286.7	322.65	362.13
182_mis_T_C	0.0	315.15	516.23
182_mis_T_G	358.3	465.22	462.30
183_mis_A_C	322.5	277.63	416.07
183_mis_A_G	250.8	510.24	751.24
183_mis_A_T	0.0	75.04	154.10
184_mis_A_C	107.5	412.69	485.41
184_mis_A_G	143.3	352.66	1502.47
184_mis_A_T	143.3	112.55	157.95
185_mis_G_A	358.3	525.25	1402.31
185_mis_G_C	107.5	97.55	50.08
185_mis_G_T	609.2	390.18	658.78
186_mis_A_C	286.7	232.61	400.66
186_mis_A_G	250.8	495.23	1864.61
186_mis_A_T	215.0	210.10	285.08
187_mis_T_A	250.8	480.22	616.40
187_mis_T_C	143.3	240.11	531.64
187_mis_T_G	645.0	502.74	508.53
188_mis_A_C	501.7	397.69	435.33
188_mis_A_G	143.3	420.20	1679.69
188_mis_A_T	179.2	157.57	327.46
189_mis_T_A	250.8	390.18	631.81
189_mis_T_C	143.3	285.13	354.43
189_mis_T_G	358.3	600.28	443.04
190_mis_C_A	394.2	870.41	862.96
190_mis_C_G	0.0	67.53	104.02
190_mis_C_T	215.0	90.04	412.22
191_mis_A_C	286.7	495.23	473.86
191_mis_A_G	358.3	217.60	739.68
191_mis_A_T	107.5	300.14	246.56
192_mis_T_A	179.2	345.16	439.18
192_mis_T_C	286.7	480.22	489.27
192_mis_T_G	788.4	637.80	708.86
193_mis_C_A	215.0	660.31	523.94
193_mis_C_G	0.0	105.05	84.75
193_mis_C_T	0.0	322.65	747.38
194_mis_G_A	143.3	562.76	631.81
194_mis_G_C	0.0	90.04	92.46
194_mis_G_T	107.5	225.11	181.07
195_mis_G_A	358.3	1328.12	1228.95
195_mis_G_C	250.8	187.59	115.57
195_mis_G_T	716.7	682.82	824.43
196_mis_C_A	0.0	375.18	570.17
196_mis_C_G	250.8	285.13	574.02
196_mis_C_T	179.2	607.78	2103.46
197_mis_T_A	107.5	60.03	235.00
197_mis_T_C	0.0	165.08	200.33
197_mis_T_G	322.5	367.67	323.61
198_mis_T_A	143.3	202.59	373.69
198_mis_T_C	286.7	270.13	624.10
198_mis_T_G	1290.0	1148.04	1552.56
199_mis_T_A	0.0	390.18	558.61
199_mis_T_C	394.2	585.27	716.56
199_mis_T_G	573.4	360.17	547.05

## Normalized table: miss_sequencer_by_string.

	s1	s2	s3
024_mis_C_A	422.9	416.29	444.26
024_mis_C_G	0.0	432.94	454.59
024_mis_C_T	761.2	691.03	743.87
025_mis_C_A	1184.0	641.08	609.56
025_mis_C_G	1353.2	1090.67	898.84
025_mis_C_T	1353.2	1140.62	1260.45
026_mis_G_A	761.2	1182.25	1332.77
026_mis_G_C	930.3	4587.46	6312.57
026_mis_G_T	4820.7	2780.78	2448.57
027_mis_T_A	338.3	624.43	692.21
027_mis_T_C	17675.9	7293.31	8378.88
027_mis_T_G	422.9	9657.81	9969.94
028_mis_C_A	253.7	299.73	588.90
028_mis_C_G	1606.9	1215.55	1033.15
028_mis_C_T	761.2	2564.32	1983.66
029_mis_G_A	592.0	616.10	681.88
029_mis_G_C	338.3	1556.91	1611.72
029_mis_G_T	4397.8	2206.31	2086.97
030_mis_T_A	338.3	208.14	185.97
030_mis_T_C	1184.0	1290.48	1270.78
030_mis_T_G	2368.1	18965.95	20094.84
031_mis_T_A	0.0	166.51	134.31
031_mis_T_C	676.6	824.24	754.20
031_mis_T_G	0.0	299.73	299.61
032_mis_T_A	0.0	158.19	185.97
032_mis_T_C	338.3	582.80	671.55
032_mis_T_G	422.9	208.14	258.29
033_mis_T_A	2198.9	890.85	878.18
033_mis_T_C	761.2	999.08	847.19
033_mis_T_G	0.0	141.54	289.28
034_mis_A_C	21904.6	8708.68	9391.37
034_mis_A_G	507.4	832.57	795.53
034_mis_A_T	1353.2	3663.31	3657.36
035_mis_C_A	5497.3	5778.04	5744.34
035_mis_C_G	0.0	58.28	144.64
035_mis_C_T	676.6	566.15	723.21
036_mis_A_C	9472.3	26850.39	30354.06
036_mis_A_G	1353.2	949.13	950.50
036_mis_A_T	253.7	199.82	175.64
037_mis_A_C	23849.8	13687.45	14805.10
037_mis_A_G	845.7	699.36	650.89
037_mis_A_T	0.0	208.14	227.29
038_mis_C_A	338.3	5461.66	5186.43
038_mis_C_G	845.7	441.26	537.24
038_mis_C_T	1014.9	557.82	650.89
039_mis_G_A	1522.3	1115.64	1146.80
039_mis_G_C	1099.5	13104.65	15259.68
039_mis_G_T	11332.9	5594.87	5558.37
040_mis_T_A	0.0	532.84	526.91
040_mis_T_C	22412.0	10040.80	10155.90
040_mis_T_G	930.3	10681.87	10796.46
041_mis_C_A	422.9	449.59	433.92
041_mis_C_G	338.3	549.50	557.90
041_mis_C_T	1099.5	1948.21	1591.06
042_mis_G_A	676.6	974.11	898.84
042_mis_G_C	676.6	6693.86	7325.06
042_mis_G_T	2537.2	2056.45	2283.27
043_mis_T_A	1184.0	707.68	1022.82
043_mis_T_C	2452.6	1906.59	1808.02
043_mis_T_G	21650.9	22321.21	23008.34
044_mis_G_A	2790.9	1873.28	1890.67
044_mis_G_C	507.4	316.38	320.28
044_mis_G_T	1014.9	4137.87	4494.22
045_mis_A_C	33744.9	15985.35	15827.92
045_mis_A_G	1099.5	2164.68	2365.92
045_mis_A_T	676.6	749.31	754.20
046_mis_C_A	338.3	3030.56	3058.14
046_mis_C_G	0.0	91.58	175.64
046_mis_C_T	2114.3	857.55	847.19
047_mis_T_A	253.7	382.98	382.27
047_mis_T_C	3044.7	18974.27	19888.21
047_mis_T_G	23173.2	7742.90	8823.13
048_mis_G_A	676.6	890.85	764.53
048_mis_G_C	338.3	249.77	227.29
048_mis_G_T	4144.1	3654.98	4018.97
049_mis_G_A	676.6	1065.69	981.50
049_mis_G_C	507.4	324.70	278.95
049_mis_G_T	1268.6	2897.34	2944.49
050_mis_G_A	4820.7	2514.36	2810.18
050_mis_G_C	253.7	324.70	206.63
050_mis_G_T	3044.7	1257.18	1601.39
051_mis_A_C	2621.8	2197.99	2386.59
051_mis_A_G	1860.6	7010.24	7139.09
051_mis_A_T	930.3	566.15	537.24
052_mis_A_C	2114.3	1806.68	1828.68
052_mis_A_G	1014.9	949.13	826.52
052_mis_A_T	0.0	133.21	103.32
053_mis_A_C	5159.0	2572.64	2727.53
053_mis_A_G	507.4	524.52	475.25
053_mis_A_T	0.0	108.23	82.65
054_mis_A_C	15477.0	10157.36	9897.61
054_mis_A_G	422.9	466.24	413.26
054_mis_A_T	507.4	133.21	165.30
055_mis_C_A	1776.0	21838.31	21675.57
055_mis_C_G	0.0	0.00	51.66
055_mis_C_T	507.4	466.24	309.95
056_mis_C_A	1268.6	641.08	630.22
056_mis_C_G	0.0	91.58	51.66
056_mis_C_T	845.7	432.94	578.57
057_mis_C_A	592.0	283.07	444.26
057_mis_C_G	0.0	91.58	51.66
057_mis_C_T	3044.7	1273.83	1188.13
058_mis_T_A	845.7	482.89	599.23
058_mis_T_C	2368.1	12563.48	13059.07
058_mis_T_G	6427.6	3080.51	3502.39
059_mis_G_A	1606.9	999.08	1105.47
059_mis_G_C	1353.2	857.55	712.88
059_mis_G_T	2029.8	9183.25	9732.31
060_mis_G_A	592.0	449.59	557.90
060_mis_G_C	23934.4	9757.72	10589.83
060_mis_G_T	5920.2	2364.50	2520.90
061_mis_C_A	422.9	241.45	392.60
061_mis_C_G	1353.2	1148.95	1250.12
061_mis_C_T	1184.0	1057.36	1146.80
062_mis_G_A	592.0	591.12	537.24
062_mis_G_C	422.9	4187.83	4721.51
062_mis_G_T	5074.4	2214.64	2055.98
063_mis_T_A	845.7	649.40	764.53
063_mis_T_C	1437.8	1989.84	1715.04
063_mis_T_G	1776.0	22795.77	22316.12
064_mis_T_A	2706.4	1090.67	1291.44
064_mis_T_C	930.3	1215.55	1074.48
064_mis_T_G	253.7	141.54	123.98
065_mis_A_C	27655.6	12172.18	12676.80
065_mis_A_G	1099.5	666.06	681.88
065_mis_A_T	1522.3	5594.87	6178.26
066_mis_C_A	2283.5	5111.98	4742.18
066_mis_C_G	0.0	83.26	123.98
066_mis_C_T	592.0	657.73	630.22
067_mis_C_A	761.2	1365.41	1281.11
067_mis_C_G	0.0	141.54	154.97
067_mis_C_T	930.3	574.47	661.22
068_mis_C_A	6427.6	3080.51	3161.45
068_mis_C_G	0.0	133.21	154.97
068_mis_C_T	845.7	716.01	671.55
069_mis_A_C	1606.9	824.24	826.52
069_mis_A_G	930.3	657.73	712.88
069_mis_A_T	0.0	141.54	113.65
070_mis_A_C	3129.2	2472.73	2355.59
070_mis_A_G	592.0	907.50	836.85
070_mis_A_T	676.6	591.12	681.88
071_mis_C_A	507.4	649.40	702.54
071_mis_C_G	0.0	41.63	61.99
071_mis_C_T	592.0	308.05	413.26
072_mis_T_A	253.7	208.14	206.63
072_mis_T_C	592.0	815.92	723.21
072_mis_T_G	761.2	299.73	382.27
073_mis_T_A	338.3	374.66	392.60
073_mis_T_C	592.0	716.01	692.21
073_mis_T_G	253.7	191.49	289.28
074_mis_A_C	338.3	1057.36	950.50
074_mis_A_G	422.9	507.87	650.89
074_mis_A_T	1099.5	749.31	671.55
075_mis_A_C	507.4	566.15	392.60
075_mis_A_G	592.0	499.54	454.59
075_mis_A_T	422.9	374.66	464.92
076_mis_T_A	676.6	1107.32	1146.80
076_mis_T_C	1606.9	815.92	981.50
076_mis_T_G	253.7	466.24	526.91
077_mis_C_A	592.0	299.73	227.29
077_mis_C_G	0.0	58.28	113.65
077_mis_C_T	592.0	557.82	568.23
078_mis_G_A	676.6	1074.02	919.51
078_mis_G_C	592.0	599.45	630.22
078_mis_G_T	1014.9	474.56	619.89
079_mis_C_A	507.4	524.52	692.21
079_mis_C_G	0.0	191.49	134.31
079_mis_C_T	338.3	316.38	361.60
080_mis_C_A	676.6	308.05	299.61
080_mis_C_G	0.0	66.61	72.32
080_mis_C_T	507.4	482.89	526.91
081_mis_T_A	0.0	449.59	526.91
081_mis_T_C	1099.5	915.83	909.18
081_mis_T_G	338.3	716.01	547.57
082_mis_T_A	338.3	333.03	237.63
082_mis_T_C	1099.5	1032.39	1198.46
082_mis_T_G	0.0	283.07	320.28
083_mis_G_A	507.4	666.06	630.22
083_mis_G_C	761.2	482.89	392.60
083_mis_G_T	1014.9	1007.41	1012.49
084_mis_C_A	0.0	291.40	278.95
084_mis_C_G	253.7	199.82	289.28
084_mis_C_T	1099.5	1323.79	1405.09
085_mis_A_C	592.0	890.85	568.23
085_mis_A_G	1522.3	1182.25	1467.08
085_mis_A_T	0.0	149.86	154.97
086_mis_G_A	253.7	865.87	898.84
086_mis_G_C	845.7	391.31	485.58
086_mis_G_T	592.0	616.10	557.90
087_mis_C_A	1522.3	482.89	454.59
087_mis_C_G	0.0	133.21	72.32
087_mis_C_T	338.3	499.54	464.92
088_mis_A_C	1691.5	1956.54	2024.98
088_mis_A_G	1184.0	957.46	1198.46
088_mis_A_T	1014.9	882.52	847.19
089_mis_C_A	253.7	333.03	402.93
089_mis_C_G	0.0	74.93	82.65
089_mis_C_T	422.9	549.50	578.57
090_mis_A_C	253.7	1365.41	1467.08
090_mis_A_G	1268.6	765.96	847.19
090_mis_A_T	676.6	641.08	547.57
091_mis_T_A	507.4	724.34	754.20
091_mis_T_C	1437.8	1240.53	1363.76
091_mis_T_G	1268.6	349.68	464.92
092_mis_C_A	507.4	258.10	268.62
092_mis_C_G	253.7	141.54	61.99
092_mis_C_T	338.3	341.35	516.58
093_mis_C_A	253.7	599.45	599.23
093_mis_C_G	0.0	133.21	185.97
093_mis_C_T	0.0	607.78	526.91
094_mis_C_A	338.3	341.35	268.62
094_mis_C_G	0.0	108.23	134.31
094_mis_C_T	338.3	324.70	289.28
095_mis_C_A	0.0	191.49	371.94
095_mis_C_G	0.0	116.56	72.32
095_mis_C_T	676.6	283.07	361.60
096_mis_C_A	422.9	333.03	278.95
096_mis_C_G	0.0	49.95	51.66
096_mis_C_T	1099.5	1074.02	1012.49
097_mis_T_A	422.9	274.75	351.27
097_mis_T_C	422.9	890.85	1012.49
097_mis_T_G	0.0	191.49	113.65
098_mis_T_A	253.7	507.87	475.25
098_mis_T_C	676.6	1007.41	1084.81
098_mis_T_G	761.2	283.07	402.93
099_mis_T_A	0.0	191.49	154.97
099_mis_T_C	1606.9	1057.36	1239.78
099_mis_T_G	507.4	299.73	340.94
100_mis_C_A	253.7	133.21	123.98
100_mis_C_G	0.0	58.28	0.00
100_mis_C_T	845.7	599.45	702.54
101_mis_G_A	2114.3	1665.14	1839.01
101_mis_G_C	592.0	616.10	609.56
101_mis_G_T	845.7	474.56	371.94
102_mis_C_A	507.4	399.63	433.92
102_mis_C_G	0.0	174.84	247.96
102_mis_C_T	1945.2	1640.16	1580.73
103_mis_C_A	0.0	233.12	185.97
103_mis_C_G	0.0	99.91	196.30
103_mis_C_T	930.3	691.03	743.87
104_mis_A_C	0.0	341.35	475.25
104_mis_A_G	1014.9	899.18	836.85
104_mis_A_T	422.9	191.49	268.62
105_mis_G_A	253.7	391.31	382.27
105_mis_G_C	0.0	108.23	154.97
105_mis_G_T	592.0	582.80	826.52
106_mis_C_A	507.4	591.12	743.87
106_mis_C_G	0.0	133.21	134.31
106_mis_C_T	0.0	283.07	340.94
107_mis_T_A	422.9	183.17	278.95
107_mis_T_C	761.2	865.87	816.19
107_mis_T_G	1522.3	990.76	1363.76
108_mis_G_A	592.0	557.82	764.53
108_mis_G_C	0.0	174.84	216.96
108_mis_G_T	0.0	466.24	526.91
109_mis_G_A	1184.0	1082.34	1105.47
109_mis_G_C	0.0	74.93	175.64
109_mis_G_T	1268.6	541.17	578.57
110_mis_C_A	2114.3	957.46	795.53
110_mis_C_G	6596.8	2597.62	2324.60
110_mis_C_T	2452.6	2206.31	2221.28
111_mis_G_A	1353.2	1240.53	1177.80
111_mis_G_C	0.0	274.75	268.62
111_mis_G_T	1014.9	549.50	774.87
112_mis_T_A	2114.3	1706.77	1673.71
112_mis_T_C	676.6	699.36	630.22
112_mis_T_G	23511.5	20156.52	20084.51
113_mis_A_C	0.0	133.21	123.98
113_mis_A_G	1099.5	1307.14	1219.12
113_mis_A_T	253.7	324.70	361.60
114_mis_A_C	0.0	174.84	175.64
114_mis_A_G	1014.9	907.50	1126.14
114_mis_A_T	338.3	649.40	526.91
115_mis_T_A	5074.4	4670.72	4504.55
115_mis_T_C	761.2	857.55	898.84
115_mis_T_G	10825.4	9482.97	9319.05
116_mis_A_C	2198.9	2289.57	2768.85
116_mis_A_G	2537.2	2222.96	2076.64
116_mis_A_T	761.2	374.66	320.28
117_mis_G_A	338.3	616.10	599.23
117_mis_G_C	592.0	399.63	402.93
117_mis_G_T	338.3	299.73	351.27
118_mis_C_A	2368.1	2297.89	1839.01
118_mis_C_G	3382.9	3430.19	2820.51
118_mis_C_T	761.2	982.43	1053.82
119_mis_G_A	1099.5	707.68	681.88
119_mis_G_C	253.7	366.33	454.59
119_mis_G_T	761.2	308.05	247.96
120_mis_A_C	1437.8	1790.03	1456.75
120_mis_A_G	2283.5	2064.77	2128.30
120_mis_A_T	253.7	399.63	547.57
121_mis_A_C	0.0	308.05	382.27
121_mis_A_G	3975.0	4012.99	3688.36
121_mis_A_T	253.7	308.05	227.29
122_mis_G_A	592.0	616.10	671.55
122_mis_G_C	0.0	258.10	216.96
122_mis_G_T	592.0	466.24	392.60
123_mis_A_C	0.0	216.47	175.64
123_mis_A_G	3298.4	3538.42	3254.43
123_mis_A_T	0.0	216.47	175.64
124_mis_G_A	930.3	932.48	816.19
124_mis_G_C	0.0	141.54	175.64
124_mis_G_T	4905.3	3963.03	4556.21
125_mis_G_A	1268.6	649.40	743.87
125_mis_G_C	422.9	399.63	382.27
125_mis_G_T	8034.5	6036.13	5475.72
126_mis_C_A	2029.8	2006.49	1043.49
126_mis_C_G	5243.6	5744.73	3905.32
126_mis_C_T	6173.9	6285.90	3688.36
127_mis_C_A	1691.5	1706.77	1498.07
127_mis_C_G	592.0	1357.09	1291.44
127_mis_C_T	2368.1	2522.69	2241.94
128_mis_C_A	4482.4	2414.45	2500.23
128_mis_C_G	3298.4	2955.62	2799.85
128_mis_C_T	2283.5	2131.38	2045.64
129_mis_G_A	1353.2	2148.03	2345.26
129_mis_G_C	338.3	574.47	578.57
129_mis_G_T	0.0	391.31	371.94
130_mis_C_A	6173.9	6002.83	6498.54
130_mis_C_G	3129.2	2722.50	2510.56
130_mis_C_T	507.4	815.92	795.53
131_mis_A_C	22158.3	19532.10	17904.56
131_mis_A_G	3721.2	3247.02	2985.81
131_mis_A_T	253.7	541.17	557.90
132_mis_C_A	2790.9	2872.37	3016.81
132_mis_C_G	1014.9	1015.74	1136.47
132_mis_C_T	676.6	491.22	650.89
133_mis_C_A	845.7	999.08	681.88
133_mis_C_G	845.7	1132.30	1033.15
133_mis_C_T	930.3	516.19	774.87
134_mis_G_A	1014.9	641.08	764.53
134_mis_G_C	338.3	316.38	309.95
134_mis_G_T	1184.0	940.80	1022.82
135_mis_A_C	1860.6	2689.20	2665.54
135_mis_A_G	2875.5	2214.64	2489.90
135_mis_A_T	592.0	707.68	681.88
136_mis_T_A	1860.6	1515.28	1332.77
136_mis_T_C	2537.2	2247.94	2179.95
136_mis_T_G	4567.0	2880.69	3285.43
137_mis_C_A	1606.9	1590.21	1363.76
137_mis_C_G	1099.5	1190.58	1167.46
137_mis_C_T	1184.0	899.18	826.52
138_mis_G_A	1606.9	1407.04	1560.06
138_mis_G_C	1014.9	1065.69	991.83
138_mis_G_T	338.3	507.87	516.58
139_mis_C_A	5074.4	4154.52	3977.64
139_mis_C_G	1606.9	1365.41	1425.75
139_mis_C_T	422.9	591.12	692.21
140_mis_C_A	5920.2	4304.39	4638.86
140_mis_C_G	1099.5	2031.47	2272.94
140_mis_C_T	930.3	840.90	867.85
141_mis_C_A	1606.9	1448.67	1415.42
141_mis_C_G	422.9	599.45	547.57
141_mis_C_T	1353.2	1581.88	1518.74
142_mis_T_A	845.7	649.40	754.20
142_mis_T_C	1606.9	1706.77	1704.70
142_mis_T_G	14631.3	12413.62	11416.35
143_mis_T_A	1945.2	1373.74	1250.12
143_mis_T_C	2706.4	2506.04	2004.32
143_mis_T_G	22327.5	20123.22	19588.60
144_mis_C_A	1268.6	1548.58	1746.03
144_mis_C_G	845.7	1032.39	785.20
144_mis_C_T	507.4	1065.69	971.16
145_mis_C_A	4989.9	4404.30	4432.23
145_mis_C_G	422.9	424.61	485.58
145_mis_C_T	845.7	724.34	785.20
146_mis_C_A	6427.6	6627.26	5795.99
146_mis_C_G	0.0	258.10	237.63
146_mis_C_T	930.3	774.29	847.19
147_mis_A_C	1014.9	865.87	599.23
147_mis_A_G	845.7	1157.27	1177.80
147_mis_A_T	0.0	258.10	340.94
148_mis_A_C	1776.0	2014.82	1684.04
148_mis_A_G	1268.6	1590.21	1529.07
148_mis_A_T	422.9	924.15	857.52
149_mis_C_A	2537.2	2189.66	2086.97
149_mis_C_G	507.4	224.79	206.63
149_mis_C_T	253.7	432.94	537.24
150_mis_A_C	2960.1	2664.22	2427.91
150_mis_A_G	1522.3	2206.31	1828.68
150_mis_A_T	0.0	208.14	216.96
151_mis_G_A	1268.6	774.29	878.18
151_mis_G_C	0.0	108.23	103.32
151_mis_G_T	930.3	915.83	867.85
152_mis_T_A	422.9	499.54	444.26
152_mis_T_C	845.7	765.96	1115.81
152_mis_T_G	5243.6	4454.25	3967.31
153_mis_T_A	507.4	441.26	320.28
153_mis_T_C	1945.2	2206.31	2014.65
153_mis_T_G	19282.8	16668.05	16871.40
154_mis_G_A	930.3	716.01	578.57
154_mis_G_C	0.0	299.73	382.27
154_mis_G_T	761.2	699.36	754.20
155_mis_C_A	1437.8	1165.60	1188.13
155_mis_C_G	2790.9	2497.71	2117.97
155_mis_C_T	3382.9	2988.93	2913.49
156_mis_G_A	1014.9	1049.04	1084.81
156_mis_G_C	845.7	707.68	671.55
156_mis_G_T	422.9	491.22	495.91
157_mis_C_A	2790.9	3488.47	3595.38
157_mis_C_G	1268.6	899.18	909.18
157_mis_C_T	422.9	591.12	516.58
158_mis_A_C	2283.5	1681.79	1653.05
158_mis_A_G	6173.9	7468.15	6663.84
158_mis_A_T	253.7	366.33	475.25
159_mis_G_A	1268.6	607.78	454.59
159_mis_G_C	422.9	224.79	278.95
159_mis_G_T	4651.6	4212.80	3399.08
160_mis_C_A	1522.3	1182.25	1498.07
160_mis_C_G	2368.1	2889.02	2314.26
160_mis_C_T	676.6	1032.39	1043.49
161_mis_C_A	3044.7	3396.89	2758.52
161_mis_C_G	676.6	832.57	795.53
161_mis_C_T	507.4	699.36	785.20
162_mis_T_A	3129.2	3022.23	2551.89
162_mis_T_C	1522.3	1581.88	1735.70
162_mis_T_G	5328.1	5603.20	5351.74
163_mis_G_A	1606.9	1548.58	1270.78
163_mis_G_C	0.0	116.56	144.64
163_mis_G_T	1606.9	1298.81	1198.46
164_mis_A_C	0.0	158.19	196.30
164_mis_A_G	1353.2	1332.11	1270.78
164_mis_A_T	422.9	716.01	671.55
165_mis_A_C	0.0	141.54	113.65
165_mis_A_G	2198.9	2256.27	2138.63
165_mis_A_T	507.4	283.07	423.59
166_mis_T_A	2114.3	2506.04	2438.24
166_mis_T_C	761.2	799.27	1002.16
166_mis_T_G	13362.7	13004.75	11054.75
167_mis_G_A	1691.5	1590.21	1808.02
167_mis_G_C	0.0	108.23	92.98
167_mis_G_T	0.0	299.73	299.61
168_mis_G_A	2706.4	3147.12	3192.45
168_mis_G_C	253.7	216.47	289.28
168_mis_G_T	0.0	457.91	495.91
169_mis_C_A	1945.2	2039.80	1932.00
169_mis_C_G	1776.0	1565.23	1446.42
169_mis_C_T	1691.5	2397.80	2355.59
170_mis_G_A	845.7	1290.48	940.17
170_mis_G_C	507.4	224.79	268.62
170_mis_G_T	338.3	516.19	402.93
171_mis_A_C	4820.7	4162.85	4215.27
171_mis_A_G	592.0	1057.36	1043.49
171_mis_A_T	422.9	607.78	702.54
172_mis_A_C	0.0	224.79	289.28
172_mis_A_G	1437.8	1606.86	1374.09
172_mis_A_T	0.0	366.33	351.27
173_mis_T_A	1353.2	1215.55	1343.10
173_mis_T_C	592.0	740.99	743.87
173_mis_T_G	5835.6	4729.00	4649.19
174_mis_G_A	930.3	907.50	950.50
174_mis_G_C	0.0	283.07	227.29
174_mis_G_T	0.0	399.63	433.92
175_mis_G_A	930.3	932.48	1115.81
175_mis_G_C	0.0	216.47	123.98
175_mis_G_T	4228.7	3471.82	3585.04
176_mis_C_A	6596.8	5894.60	5537.70
176_mis_C_G	2368.1	2439.43	1725.37
176_mis_C_T	3552.1	4329.36	4225.60
177_mis_G_A	845.7	1065.69	1022.82
177_mis_G_C	253.7	158.19	237.63
177_mis_G_T	338.3	749.31	712.88
178_mis_C_A	6004.7	6102.74	4804.17
178_mis_C_G	1099.5	1282.16	1115.81
178_mis_C_T	1014.9	849.22	1043.49
179_mis_T_A	1014.9	1665.14	1539.40
179_mis_T_C	422.9	732.66	774.87
179_mis_T_G	2706.4	3355.26	3430.07
180_mis_A_C	2029.8	1040.71	1157.13
180_mis_A_G	422.9	341.35	454.59
180_mis_A_T	1184.0	765.96	681.88
181_mis_A_C	930.3	1065.69	1012.49
181_mis_A_G	507.4	358.01	609.56
181_mis_A_T	845.7	516.19	454.59
182_mis_T_A	1437.8	1615.19	1115.81
182_mis_T_C	592.0	466.24	475.25
182_mis_T_G	2114.3	2281.24	1901.00
183_mis_A_C	1268.6	1182.25	1312.11
183_mis_A_G	338.3	333.03	475.25
183_mis_A_T	676.6	566.15	619.89
184_mis_A_C	1353.2	1207.23	1084.81
184_mis_A_G	676.6	674.38	826.52
184_mis_A_T	0.0	374.66	361.60
185_mis_G_A	1099.5	1173.92	1115.81
185_mis_G_C	253.7	349.68	185.97
185_mis_G_T	1184.0	1223.88	1136.47
186_mis_A_C	1184.0	1307.14	1260.45
186_mis_A_G	422.9	549.50	764.53
186_mis_A_T	422.9	474.56	402.93
187_mis_T_A	1606.9	1556.91	1570.39
187_mis_T_C	761.2	557.82	692.21
187_mis_T_G	2368.1	2231.29	2076.64
188_mis_A_C	1184.0	1631.84	1343.10
188_mis_A_G	592.0	341.35	578.57
188_mis_A_T	1014.9	699.36	537.24
189_mis_T_A	1184.0	999.08	1260.45
189_mis_T_C	930.3	890.85	764.53
189_mis_T_G	2790.9	1823.33	1704.70
190_mis_C_A	2198.9	2048.12	1766.69
190_mis_C_G	0.0	149.86	92.98
190_mis_C_T	0.0	208.14	247.96
191_mis_A_C	2790.9	2222.96	2117.97
191_mis_A_G	338.3	516.19	382.27
191_mis_A_T	507.4	557.82	650.89
192_mis_T_A	1437.8	1057.36	1219.12
192_mis_T_C	2114.3	1290.48	1405.09
192_mis_T_G	2621.8	2339.52	2345.26
193_mis_C_A	676.6	874.20	805.86
193_mis_C_G	0.0	516.19	371.94
193_mis_C_T	0.0	166.51	206.63
194_mis_G_A	676.6	391.31	433.92
194_mis_G_C	507.4	532.84	309.95
194_mis_G_T	338.3	283.07	320.28
195_mis_G_A	676.6	691.03	640.56
195_mis_G_C	1099.5	982.43	847.19
195_mis_G_T	1437.8	1448.67	1394.76
196_mis_C_A	1099.5	674.38	609.56
196_mis_C_G	2368.1	2048.12	2500.23
196_mis_C_T	2283.5	1623.51	1684.04
197_mis_T_A	338.3	233.12	154.97
197_mis_T_C	507.4	241.45	382.27
197_mis_T_G	1776.0	1373.74	1177.80
198_mis_T_A	0.0	499.54	320.28
198_mis_T_C	253.7	532.84	433.92
198_mis_T_G	4905.3	4321.04	4463.22
199_mis_T_A	0.0	158.19	175.64
199_mis_T_C	1606.9	1407.04	1198.46
199_mis_T_G	1691.5	1914.91	1787.36

## Normalized table: miss_reads_by_ref_nt.

	s1	s2	s3
A	77570	160363	263245
C	432402	392806	420662
G	415082	341318	214773
T	74947	105513	101319

## Normalized table: miss_indexes_by_ref_nt.

	s1	s2	s3
A	80879	162488	261477
C	422131	385643	411655
G	415610	335137	214218
T	81380	116732	112651

## Normalized table: miss_sequencer_by_ref_nt.

	s1	s2	s3
A	276049	240546	243246
C	220822	238690	227366
G	171516	168595	175719
T	331614	352169	353669

## Normalized table: miss_reads_by_hit_nt.

	s1	s2	s3
A	417789	504509	314618
C	82669	71652	75899
G	75975	179391	285063
T	423567	244448	324420

## Normalized table: miss_indexes_by_hit_nt.

	s1	s2	s3
A	401777	489912	310542
C	87114	80025	84855
G	81165	185457	287500
T	429943	244607	317103

## Normalized table: miss_sequencer_by_hit_nt.

	s1	s2	s3
A	193336	206053	201806
C	325947	292324	303055
G	315545	341762	335992
T	165173	159862	159147

## Normalized table: miss_reads_by_type.

	s1	s2	s3
A_C	46168	31467	32850
A_G	23952	113640	211555
A_T	7450	15255	18840
C_A	348760	226116	134895
C_G	12193	28143	38221
C_T	71449	138546	247546
G_A	61397	239912	147196
G_C	9017	10760	9544
G_T	344668	90646	58033
T_A	7632	38481	32527
T_C	27484	29424	33505
T_G	39831	37608	35287

## Normalized table: miss_indexes_by_type.

	s1	s2	s3
A_C	46370	33886	36283
A_G	26088	111772	205727
A_T	8421	16830	19467
C_A	333441	221248	134263
C_G	12255	28873	38671
C_T	76435	135521	238720
G_A	60381	230253	143409
G_C	10141	12628	11893
G_T	345087	92256	58916
T_A	7955	38410	32869
T_C	30603	33511	36680
T_G	42822	44811	43102

## Normalized table: miss_sequencer_by_type.

	s1	s2	s3
A_C	201370	152319	155076
A_G	55734	61943	61390
A_T	18945	26284	26779
C_A	108085	127000	122553
C_G	50829	50554	45893
C_T	61908	61136	58921
G_A	46938	43419	44095
G_C	40257	52735	58177
G_T	84320	72442	73447
T_A	38312	35634	35158
T_C	84320	87270	89802
T_G	208982	229265	228709

## Normalized table: miss_reads_by_trans.

	s1	s2	s3
transition	184282	521523	639803
transversion	815718	478477	360197

## Normalized table: miss_indexes_by_trans.

	s1	s2	s3
transition	193507	511056	624536
transversion	806493	488944	375464

## Normalized table: miss_sequencer_by_trans.

	s1	s2	s3
transition	248901	253767	254208
transversion	751099	746233	745792

## Normalized table: miss_reads_by_strength.

	s1	s2	s3
strong_strong	21209	38904	47765
strong_weak	826274	695220	587671
weak_strong	137435	212140	313197
weak_weak	15082	53736	51367

## Normalized table: miss_indexes_by_strength.

	s1	s2	s3
strong_strong	22397	41502	50564
strong_weak	815344	679278	575309
weak_strong	145883	223980	321791
weak_weak	16376	55241	52336

## Normalized table: miss_sequencer_by_strength.

	s1	s2	s3
strong_strong	91086	103289	104070
strong_weak	301252	303996	299015
weak_strong	550406	530797	534977
weak_weak	57256	61918	61938

## Normalized table: insert_reads_by_position.

	s1	s2	s3
24	0	0	1688.3
25	0	6494	0.0
26	0	3711	0.0
27	0	11132	0.0
28	0	0	1688.3
29	0	0	519.5
30	0	15770	10129.9
35	0	0	3116.9
36	0	6494	1039.0
42	0	12987	0.0
44	0	0	649.4
45	0	0	1688.3
46	127660	8349	4675.3
47	0	4638	389.6
48	0	144712	107662.3
50	0	0	2597.4
51	85106	179963	450000.0
52	0	0	18701.3
55	0	0	33246.8
58	0	0	389.6
59	0	0	909.1
61	0	0	389.6
62	0	2783	0.0
69	0	0	649.4
72	0	0	62727.3
81	0	0	8311.7
91	0	66790	90649.4
92	127660	177180	28441.6
93	0	0	4675.3
97	0	241187	97792.2
100	0	21336	0.0
105	0	0	1039.0
110	0	0	519.5
120	0	0	519.5
123	0	0	41558.4
124	0	0	519.5
126	148936	0	0.0
130	0	0	649.4
132	0	9276	0.0
134	85106	0	0.0
137	0	0	1298.7
138	0	0	519.5
142	0	0	4026.0
144	0	0	11688.3
148	0	0	2597.4
149	0	11132	0.0
151	0	11132	0.0
154	0	59369	0.0
156	0	5566	0.0
171	148936	0	519.5
174	148936	0	0.0
177	0	0	1039.0
182	127660	0	0.0
190	0	0	779.2

## Normalized table: insert_indexes_by_position.

	s2	s3
30	23077	10499
46	0	5249
48	146154	101050
51	192308	469816
52	0	15748
55	0	20997
72	0	51181
81	0	10499
91	61538	94488
92	153846	45932
93	0	7874
97	307692	108924
100	23077	0
123	0	31496
142	0	9186
144	0	11811
148	0	5249
151	30769	0
154	61538	0

## Normalized table: insert_sequencer_by_position.

	s2	s3
29	100000	78431
34	0	58824
35	75000	0
42	0	78431
46	0	58824
48	125000	98039
51	75000	98039
55	0	58824
66	100000	0
92	400000	274510
97	0	58824
149	0	78431
151	0	58824
156	125000	0

## Normalized table: insert_reads_by_nt.

	s1	s2	s3
A	234043	191095	499351
C	404255	221707	92597
G	234043	246753	130390
T	127660	340445	277662

## Normalized table: insert_indexes_by_nt.

	s2	s3
A	192308	501312
C	176923	91864
G	238462	116798
T	392308	290026

## Normalized table: insert_sequencer_by_nt.

	s2	s3
A	75000	156863
C	575000	470588
G	350000	313725
T	0	58824

## Normalized table: delete_reads_by_position.

s1	s2	s3

## Normalized table: delete_indexes_by_position.

s1	s2	s3

## Normalized table: delete_sequencer_by_position.

s1	s2	s3

## Normalized table: delete_reads_by_nt.

s1	s2	s3

## Normalized table: delete_indexes_by_nt.

s1	s2	s3

## Normalized table: delete_sequencer_by_nt.

s1	s2	s3

7 Print normalized plots

for (t in 1:length(triplets[["normalized"]])) {
  message("Normalized table: ", table_name, ".")
  print(data_plots[["normal"]][t])
}

## Normalized table: delete_sequencer_by_nt.

## Error in print(data_plots[["normal"]][t]): object 'data_plots' not found

pander::pander(sessionInfo())

R version 3.6.1 (2019-07-05)

Platform: x86_64-pc-linux-gnu (64-bit)

locale: LC_CTYPE=en_US.UTF-8, LC_NUMERIC=C, LC_TIME=en_US.UTF-8, LC_COLLATE=en_US.UTF-8, LC_MONETARY=en_US.UTF-8, LC_MESSAGES=en_US.UTF-8, LC_PAPER=en_US.UTF-8, LC_NAME=C, LC_ADDRESS=C, LC_TELEPHONE=C, LC_MEASUREMENT=en_US.UTF-8 and LC_IDENTIFICATION=C

attached base packages: parallel, stats, graphics, grDevices, utils, datasets, methods and base

other attached packages: errRt(v.1.0), tidyr(v.1.0.0), dplyr(v.0.8.3), hpgltools(v.1.0), Biobase(v.2.46.0) and BiocGenerics(v.0.32.0)

loaded via a namespace (and not attached): tidyselect(v.0.2.5), lme4(v.1.1-21), RSQLite(v.2.1.4), AnnotationDbi(v.1.48.0), grid(v.3.6.1), BiocParallel(v.1.20.0), devtools(v.2.2.1), munsell(v.0.5.0), codetools(v.0.2-16), withr(v.2.1.2), colorspace(v.1.4-1), GOSemSim(v.2.12.0), highr(v.0.8), knitr(v.1.26), rstudioapi(v.0.10), stats4(v.3.6.1), DOSE(v.3.12.0), labeling(v.0.3), urltools(v.1.7.3), GenomeInfoDbData(v.1.2.2), polyclip(v.1.10-0), bit64(v.0.9-7), farver(v.2.0.1), rprojroot(v.1.3-2), vctrs(v.0.2.1), xfun(v.0.11), BiocFileCache(v.1.10.2), R6(v.2.4.1), doParallel(v.1.0.15), GenomeInfoDb(v.1.22.0), graphlayouts(v.0.5.0), locfit(v.1.5-9.1), bitops(v.1.0-6), fgsea(v.1.12.0), gridGraphics(v.0.4-1), DelayedArray(v.0.12.0), assertthat(v.0.2.1), scales(v.1.1.0), ggraph(v.2.0.0), enrichplot(v.1.6.0), gtable(v.0.3.0), sva(v.3.34.0), processx(v.3.4.1), tidygraph(v.1.1.2), rlang(v.0.4.2), zeallot(v.0.1.0), genefilter(v.1.68.0), splines(v.3.6.1), rtracklayer(v.1.46.0), lazyeval(v.0.2.2), europepmc(v.0.3), BiocManager(v.1.30.10), yaml(v.2.2.0), reshape2(v.1.4.3), GenomicFeatures(v.1.38.0), backports(v.1.1.5), qvalue(v.2.18.0), clusterProfiler(v.3.14.0), tools(v.3.6.1), usethis(v.1.5.1), ggplotify(v.0.0.4), ggplot2(v.3.2.1), ellipsis(v.0.3.0), gplots(v.3.0.1.1), RColorBrewer(v.1.1-2), sessioninfo(v.1.1.1), ggridges(v.0.5.1), Rcpp(v.1.0.3), plyr(v.1.8.5), base64enc(v.0.1-3), progress(v.1.2.2), zlibbioc(v.1.32.0), purrr(v.0.3.3), RCurl(v.1.95-4.12), ps(v.1.3.0), prettyunits(v.1.0.2), openssl(v.1.4.1), viridis(v.0.5.1), cowplot(v.1.0.0), S4Vectors(v.0.24.1), SummarizedExperiment(v.1.16.0), ggrepel(v.0.8.1), colorRamps(v.2.3), fs(v.1.3.1), variancePartition(v.1.16.0), magrittr(v.1.5), data.table(v.1.12.8), DO.db(v.2.9), openxlsx(v.4.1.4), triebeard(v.0.3.0), matrixStats(v.0.55.0), pkgload(v.1.0.2), hms(v.0.5.2), evaluate(v.0.14), xtable(v.1.8-4), pbkrtest(v.0.4-7), XML(v.3.98-1.20), IRanges(v.2.20.1), gridExtra(v.2.3), testthat(v.2.3.1), compiler(v.3.6.1), biomaRt(v.2.42.0), tibble(v.2.1.3), KernSmooth(v.2.23-16), crayon(v.1.3.4), minqa(v.1.2.4), htmltools(v.0.4.0), mgcv(v.1.8-31), DBI(v.1.0.0), tweenr(v.1.0.1), dbplyr(v.1.4.2), MASS(v.7.3-51.4), rappdirs(v.0.3.1), boot(v.1.3-23), Matrix(v.1.2-18), readr(v.1.3.1), cli(v.2.0.0), gdata(v.2.18.0), igraph(v.1.2.4.2), GenomicRanges(v.1.38.0), pkgconfig(v.2.0.3), rvcheck(v.0.1.7), GenomicAlignments(v.1.22.1), xml2(v.1.2.2), foreach(v.1.4.7), annotate(v.1.64.0), XVector(v.0.26.0), stringr(v.1.4.0), callr(v.3.4.0), digest(v.0.6.23), Biostrings(v.2.54.0), rmarkdown(v.1.18), fastmatch(v.1.1-0), edgeR(v.3.28.0), curl(v.4.3), Rsamtools(v.2.2.1), gtools(v.3.8.1), nloptr(v.1.2.1), lifecycle(v.0.1.0), nlme(v.3.1-143), jsonlite(v.1.6), desc(v.1.2.0), viridisLite(v.0.3.0), askpass(v.1.1), limma(v.3.42.0), fansi(v.0.4.0), pillar(v.1.4.3), lattice(v.0.20-38), httr(v.1.4.1), pkgbuild(v.1.0.6), survival(v.3.1-8), GO.db(v.3.10.0), glue(v.1.3.1), remotes(v.2.1.0), zip(v.2.0.4), iterators(v.1.0.12), pander(v.0.6.3), bit(v.1.1-14), ggforce(v.0.3.1), stringi(v.1.4.3), blob(v.1.2.0), caTools(v.1.17.1.3) and memoise(v.1.1.0)

message(paste0("This is hpgltools commit: ", get_git_commit()))

## If you wish to reproduce this exact build of hpgltools, invoke the following:

## > git clone http://github.com/abelew/hpgltools.git

## > git reset defea68c4df789830e6d759243e1f973d2d9dca7

## This is hpgltools commit: Fri Dec 27 17:07:39 2019 -0500: defea68c4df789830e6d759243e1f973d2d9dca7

this_save <- paste0(gsub(pattern="\\.Rmd", replace="", x=rmd_file), "-v", ver, ".rda.xz")

## Error in gsub(pattern = "\\.Rmd", replace = "", x = rmd_file): object 'rmd_file' not found

message(paste0("Saving to ", this_save))

## Error in paste0("Saving to ", this_save): object 'this_save' not found

tmp <- sm(saveme(filename=this_save))

## Error in file.path(getwd(), directory, filename): object 'this_save' not found

loadme(filename=this_save)

---
title: "Counting RT mutations from illumina sequencing data."
author: "atb abelew@gmail.com"
date: "`r Sys.Date()`"
output:
  html_document:
    code_download: true
    code_folding: show
    fig_caption: true
    fig_height: 7
    fig_width: 7
    highlight: tango
    keep_md: false
    mode: selfcontained
    number_sections: true
    self_contained: true
    theme: readable
    toc: true
    toc_float:
      collapsed: false
      smooth_scroll: false
  rmdformats::readthedown:
    code_download: true
    code_folding: show
    df_print: paged
    fig_caption: true
    fig_height: 7
    fig_width: 7
    highlight: tango
    width: 300
    keep_md: false
    mode: selfcontained
    toc_float: true
  BiocStyle::html_document:
    code_download: true
    code_folding: show
    fig_caption: true
    fig_height: 7
    fig_width: 7
    highlight: tango
    keep_md: false
    mode: selfcontained
    toc_float: true
---

<style type="text/css">
body, td {
  font-size: 16px;
}
code.r{
  font-size: 16px;
}
pre {
 font-size: 16px
}
</style>

```{r options, include=FALSE}
library("hpgltools")
tt <- devtools::load_all("/data/hpgltools")
knitr::opts_knit$set(width=120,
                     progress=TRUE,
                     verbose=TRUE,
                     echo=TRUE)
knitr::opts_chunk$set(error=TRUE,
                      dpi=96)
old_options <- options(digits=4,
                       stringsAsFactors=FALSE,
                       knitr.duplicate.label="allow")
ggplot2::theme_set(ggplot2::theme_bw(base_size=10))
rundate <- format(Sys.Date(), format="%Y%m%d")
previous_file <- "index.Rmd"
ver <- "20191201"

##tmp <- sm(loadme(filename=paste0(gsub(pattern="\\.Rmd", replace="", x=previous_file), "-v", ver, ".rda.xz")))
##rmd_file <- "03_expression_infection_20180822.Rmd"
```

# Calculating error rates.

I wrote the function 'create_matrices()' to collect mutation counts.  At least
in theory the results from it should be able to address most/any question
regarding the counts of mutations observed in the data.

```{r testing}
devtools::load_all("errRt")

triplets <- create_matrices(sample_sheet="sample_sheets/all_samples.xlsx",
                            ident_column="identtable", mut_column="mutationtable",
                            min_reads=3, min_indexes=3, min_sequencer=10,
                            min_position=24, prune_n=TRUE, verbose=TRUE)
triplet_plots <- barplot_matrices(triplets)
summary(triplets)
quintuplets <- create_matrices(sample_sheet="sample_sheets/all_samples.xlsx",
                               ident_column="identtable", mut_column="mutationtable",
                               min_reads=3, min_indexes=5, min_sequencer=10,
                               min_position=24, prune_n=TRUE, verbose=TRUE)
quintuplet_plots <- barplot_matrices(quintuplets)
summary(triplets)
```

# Questions from Dr. DeStefano

I think what is best is to get the number of recovered mutations of each type
from each data set.  That would be A to T, A to G, A to C; T to A, T to G, T to
C; G to A, G to C, G to T; and C to A, C to G, C to T; as well as deletions and
insertions.  I would then need the sum number of the reads that met all our
criteria (i.e. at least 3 good recovered reads for that 14 nt index).  Each set
of 3 or more would ct as "1" read of that particular index so I would need the
total with this in mind.  I also need to know the total number of nucleotides
that were in the region we decided to consider in the analysis.  We may want to
try this for 3 or more and 5 or more recovered indexes if it is not hard.  This
information does not include specific positions on the template where errors
occurred but we can look at that latter.  Right now I just want to get a general
error rate and type of error.  It would basically be calculated by dividing the
number of recovered mutations of a particular type by sum number of the reads
times the number of nucleotides screened in the template.  As it ends up, this
number does not really have a lot of meaning but it can be used to calculate the
overall mutation rate as well as the rate for transversions, transitions, and
deletions and insertions.

# Answers

In order to address those queries, I invoked create_matrices() with a minimum
index count of 3 and 5.  It should be noted that this is not the same as
requiring 3 or 5 reads per index.  In both cases I require 3 reads per index.

## Recovered mutations of each type

I am interpreting this question as the number of indexes recovered for each
mutation type.  I collect this information in 2 ways of interest: the indexes by
type which are deemed to be from the RT and from the sequencer.  In addition, I
calculate a normalized (cpm) version of this information which may be used to look for
changes across samples.

### Mutations by RT index

This following block should print out tables of the numbers of mutant indexes
observed for each type for the RT and the sequencer.  One would hope that the
sequencer will be consistent for all samples, but I think the results will
instead suggest that my metric is not yet stringent enough.

```{r mutation_index_count, results='asis'}
knitr::kable(triplets[["matrices"]][["miss_indexes_by_type"]])

knitr::kable(triplets[["matrices"]][["miss_sequencer_by_type"]])

knitr::kable(quintuplets[["matrices"]][["miss_indexes_by_type"]])

knitr::kable(quintuplets[["matrices"]][["miss_sequencer_by_type"]])
```

Plots of this information

```{r mutation_index_count_plots}
triplet_plots[["matrices"]][["miss_indexes_by_type"]]
triplet_plots[["normal"]][["miss_indexes_by_type"]]

quintuplet_plots[["matrices"]][["miss_indexes_by_type"]]
quintuplet_plots[["normal"]][["miss_indexes_by_type"]]
```

This suggests to me that this information needs to be normalized in some more
sensible fashion.  Thus the following:

### Mutations by RT index, post normalization

The same numbers may be expressed in the context of the number of indexes
observed / sample and/or as a cpm across samples.  Thus in the first instance
one can look at the apparent error rate for each sample, and in the second
instance one may look for relative changes in apparent error rate across
samples.

#### Rewriting the matrices as cpm to account for library sizes.

```{r mutation_index_normalized, results='asis'}
knitr::kable(triplets[["normalized"]][["miss_indexes_by_type"]])

knitr::kable(triplets[["normalized"]][["miss_sequencer_by_type"]])

knitr::kable(quintuplets[["normalized"]][["miss_indexes_by_type"]])

knitr::kable(quintuplets[["normalized"]][["miss_sequencer_by_type"]])
```

#### Rewriting the matrices by dividing by all indexes

This I think starts to address the later text in your query.

```{r mutation_index_normalized_by_counts, results='asis'}
knitr::kable(triplets[["matrices_by_counts"]][["miss_indexes_by_type"]])

knitr::kable(triplets[["matrices_by_counts"]][["miss_sequencer_by_type"]])

knitr::kable(quintuplets[["matrices_by_counts"]][["miss_indexes_by_type"]])

knitr::kable(quintuplets[["matrices_by_counts"]][["miss_sequencer_by_type"]])
```

#### Rewriting the matrices by dividing by all indexes and cpm

I think this might prove to be where we get the most meaningful results.

The nicest thing in it is that after accounting for library sizes and total
indexes observed, we finally see that the sequencer error is mostly consistent
across all samples and mutation types -- with a couple of notable exceptions.

By the same token, for the mutations which _are_ identical for the sequencer, we
have some which are decidedly different for the non-sequencer data.  The most
notable examples I think are A to G but _not G to A; and C to T.

```{r mutation_index_cpm_by_counts, results='asis'}
knitr::kable(triplets[["normalized_by_counts"]][["miss_indexes_by_type"]])

knitr::kable(triplets[["normalized_by_counts"]][["miss_sequencer_by_type"]])

knitr::kable(quintuplets[["normalized_by_counts"]][["miss_indexes_by_type"]])

knitr::kable(quintuplets[["normalized_by_counts"]][["miss_sequencer_by_type"]])
```

### Indels by RT index

The following blocks will repeat the above, but looking for insertions.
This data does not observe sufficient deletions to make a proper count for them.

```{r insert_index_count, results='asis'}
knitr::kable(triplets[["matrices"]][["insert_indexes_by_nt"]])

knitr::kable(triplets[["matrices"]][["insert_sequencer_by_nt"]])

knitr::kable(quintuplets[["matrices"]][["insert_indexes_by_nt"]])

knitr::kable(quintuplets[["matrices"]][["insert_sequencer_by_nt"]])
```

Plots of this information

```{r insert_index_count_plots}
triplet_plots[["matrices"]][["insert_indexes_by_nt"]]
triplet_plots[["normal"]][["insert_indexes_by_nt"]]

quintuplet_plots[["matrices"]][["insert_indexes_by_nt"]]
quintuplet_plots[["matrices"]][["insert_sequencer_by_nt"]]
quintuplet_plots[["normal"]][["insert_indexes_by_nt"]]
quintuplet_plots[["normal"]][["insert_sequencer_by_nt"]]
```

### Insertions by RT index, post normalization

#### Rewriting the matrices as cpm to account for library sizes.

```{r insert_index_normalized, results='asis'}
knitr::kable(triplets[["normalized"]][["insert_indexes_by_nt"]])

knitr::kable(triplets[["normalized"]][["insert_sequencer_by_nt"]])

knitr::kable(quintuplets[["normalized"]][["insert_indexes_by_nt"]])

knitr::kable(quintuplets[["normalized"]][["insert_sequencer_by_nt"]])
```

#### Rewriting the matrices by dividing by all indexes

I think that there are few enough insertion events that this gets a bit messed
up.  I will double check the logic of this, but that is my initial guess given
how few insertions I was seeing when reading the outputs manually.
Unfortunately, this means that for these I also cannot provide a cpm measurement.

```{r insert_index_normalized_by_counts, results='asis'}
knitr::kable(triplets[["matrices_by_counts"]][["insert_indexes_by_nt"]])

knitr::kable(triplets[["matrices_by_counts"]][["insert_sequencer_by_nt"]])

knitr::kable(quintuplets[["matrices_by_counts"]][["insert_indexes_by_nt"]])

knitr::kable(quintuplets[["matrices_by_counts"]][["insert_sequencer_by_nt"]])
```

The following is my previous writing of this worksheet which just dumped the
various tables.

# Print raw tables

```{r raw, results='asis'}
for (t in 1:length(triplets[["matrices"]])) {
  table_name <- names(triplets[["matrices"]])[t]
  message("Raw table: ", table_name, ".")
  print(knitr::kable(triplets[["matrices"]][t]))
}
```

# Print raw plots

```{r raw_plots}
for (t in 1:length(triplets[["matrices"]])) {
  message("Raw table: ", table_name, ".")
  print(data_plots[["matrices"]][t])
}
```

# Print normalized tables

```{r norm, results='asis'}
for (t in 1:length(triplets[["normalized"]])) {
  table_name <- names(triplets[["normalized"]])[t]
  message("Normalized table: ", table_name, ".")
  print(knitr::kable(triplets[["normalized"]][t]))
}
```

# Print normalized plots

```{r norm_plots}
for (t in 1:length(triplets[["normalized"]])) {
  message("Normalized table: ", table_name, ".")
  print(data_plots[["normal"]][t])
}
```

```{r saveme}
pander::pander(sessionInfo())
message(paste0("This is hpgltools commit: ", get_git_commit()))
this_save <- paste0(gsub(pattern="\\.Rmd", replace="", x=rmd_file), "-v", ver, ".rda.xz")
message(paste0("Saving to ", this_save))
tmp <- sm(saveme(filename=this_save))
```


```{r loadme, eval=FALSE}
loadme(filename=this_save)
```


Counting RT mutations from illumina sequencing data.

atb abelew@gmail.com

2020-01-06