Input data and parameters 

QualiMap command line

qualimap bamqc -bam /Users/strigg/Desktop/20200429/Sealice_F1_S20_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_F1_S20_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/strigg/analyses/20200427/TG_PE_FASTQS/cat_lanes/Sealice_F1_S20_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 19:00:10 PDT 2020
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: /Users/strigg/Desktop/20200429/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam

Summary 

Globals

Reference size 506,970,227
Number of reads 78,560,122
Mapped reads 78,560,122 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 78,560,122 / 100%
Mapped reads, first in pair 39,280,061 / 50%
Mapped reads, second in pair 39,280,061 / 50%
Mapped reads, both in pair 78,560,122 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 130 / 106.93
Duplicated reads (estimated) 38,027,809 / 48.41%
Duplication rate 47.24%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 3,310,635,970 / 39.85%
Number/percentage of C's 842,628,577 / 10.14%
Number/percentage of T's 3,309,294,141 / 39.83%
Number/percentage of G's 845,982,029 / 10.18%
Number/percentage of N's 55,673 / 0%
GC Percentage 20.32%

Coverage

Mean 16.4619
Standard Deviation 61.5992

Mapping Quality

Mean Mapping Quality 18.05

Insert size

Mean 144.66
Standard Deviation 81.22
P25/Median/P75 86 / 128 / 183

Mismatches and indels

General error rate 21.76%
Mismatches 1,723,794,603
Insertions 51,232,487
Mapped reads with at least one insertion 42.26%
Deletions 22,505,941
Mapped reads with at least one deletion 23.69%
Homopolymer indels 56.51%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
Cr_scaffold0000001 36897007 624817582 16.9341 54.9143
Cr_scaffold0000002 35124817 564360503 16.0673 54.5975
Cr_scaffold0000003 33138466 547480744 16.521 44.3544
Cr_scaffold0000004 31456035 539156134 17.14 42.2715
Cr_scaffold0000005 30612693 488397980 15.9541 32.4117
Cr_scaffold0000006 30259679 492505596 16.276 32.3946
Cr_scaffold0000007 29872177 477042754 15.9695 45.2434
Cr_scaffold0000008 27803016 467043496 16.7983 109.7299
Cr_scaffold0000009 25126635 405353812 16.1324 40.2466
Cr_scaffold0000010 24815513 402306836 16.2119 38.0215
Cr_scaffold0000011 35794548 626880636 17.5133 30.1117
Cr_scaffold0000012 22957860 344899879 15.0232 23.1358
Cr_scaffold0000013 21502856 329115322 15.3057 24.0611
Cr_scaffold0000014 21148584 349238459 16.5136 53.7005
Cr_scaffold0000015 19091682 319360575 16.7277 83.6603
Cr_scaffold0000016 18525937 295706625 15.9618 51.7649
Cr_scaffold0000017 17562062 308487706 17.5656 181.6498
Cr_scaffold0000018 14680182 233233549 15.8876 53.0525
Cr_scaffold0000019 14290452 261793449 18.3195 86.1002
Cr_scaffold0000020 8286978 129928875 15.6787 37.7286
Cr_scaffold0000021 8023048 138595088 17.2746 34.6983

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