Input data and parameters 

QualiMap command line

qualimap bamqc -bam /Users/strigg/Desktop/20200429/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam -nw 400 -hm 3

Alignment

Command line: "bismark --score_min L,0,-0.6 -p 4 --non_directional --genome /gscratch/srlab/strigg/data/Caligus/GENOMES -1 /gscratch/scrubbed/strigg/analyses/20200427/TG_PE_FASTQS/cat_lanes/Sealice_F2_S22_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/strigg/analyses/20200427/TG_PE_FASTQS/cat_lanes/Sealice_F2_S22_R2_001_val_2.fq.gz"
Draw chromosome limits: no
Analyze overlapping paired-end reads: no
Program: Bismark (v0.22.3)
Analysis date: Wed Apr 29 19:05:07 PDT 2020
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: /Users/strigg/Desktop/20200429/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam

Summary 

Globals

Reference size 506,970,227
Number of reads 52,851,202
Mapped reads 52,851,202 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 52,851,202 / 100%
Mapped reads, first in pair 26,425,601 / 50%
Mapped reads, second in pair 26,425,601 / 50%
Mapped reads, both in pair 52,851,202 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 130 / 103.31
Duplicated reads (estimated) 26,598,716 / 50.33%
Duplication rate 51.98%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 2,115,706,099 / 39.17%
Number/percentage of C's 583,259,551 / 10.8%
Number/percentage of T's 2,115,926,575 / 39.17%
Number/percentage of G's 586,828,841 / 10.86%
Number/percentage of N's 37,214 / 0%
GC Percentage 21.66%

Coverage

Mean 10.698
Standard Deviation 39.3661

Mapping Quality

Mean Mapping Quality 18.31

Insert size

Mean 128.08
Standard Deviation 67.81
P25/Median/P75 80 / 115 / 160

Mismatches and indels

General error rate 22.29%
Mismatches 1,150,228,632
Insertions 31,916,330
Mapped reads with at least one insertion 39.94%
Deletions 13,183,016
Mapped reads with at least one deletion 20.88%
Homopolymer indels 56.21%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
Cr_scaffold0000001 36897007 404936863 10.9748 33.0964
Cr_scaffold0000002 35124817 362600191 10.3232 31.3745
Cr_scaffold0000003 33138466 352323453 10.6319 30.8397
Cr_scaffold0000004 31456035 352846366 11.2171 30.6738
Cr_scaffold0000005 30612693 315959864 10.3212 23.5614
Cr_scaffold0000006 30259679 321335601 10.6193 23.2171
Cr_scaffold0000007 29872177 306410488 10.2574 24.0582
Cr_scaffold0000008 27803016 297609720 10.7042 66.7805
Cr_scaffold0000009 25126635 262593429 10.4508 27.2482
Cr_scaffold0000010 24815513 261394168 10.5335 24.9593
Cr_scaffold0000011 35794548 414241160 11.5727 22.8389
Cr_scaffold0000012 22957860 222970252 9.7122 17.7137
Cr_scaffold0000013 21502856 213757476 9.9409 18.6512
Cr_scaffold0000014 21148584 225352401 10.6557 35.4431
Cr_scaffold0000015 19091682 209103661 10.9526 54.8611
Cr_scaffold0000016 18525937 196801680 10.623 73.4493
Cr_scaffold0000017 17562062 198184660 11.2848 92.4514
Cr_scaffold0000018 14680182 149310118 10.1709 31.1006
Cr_scaffold0000019 14290452 175609581 12.2886 57.1096
Cr_scaffold0000020 8286978 86196812 10.4015 30.0225
Cr_scaffold0000021 8023048 94023759 11.7192 24.9187

Coverage across reference 

Coverage Histogram 

Coverage Histogram (0-50X) 

Genome Fraction Coverage 

Duplication Rate Histogram 

Mapped Reads Nucleotide Content 

Mapped Reads GC-content Distribution 

Homopolymer Indels 

Mapping Quality Across Reference 

Mapping Quality Histogram 

Insert Size Across Reference 

Insert Size Histogram