BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10525239.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.result/quality.files/genome_results.txt
>>>>>>> Reference
number of bases = 3,095,693,983 bp
number of contigs = 25
>>>>>>> Globals
number of windows = 424
number of reads = 939,287
number of mapped reads = 853,768 (90.9%)
number of supplementary alignments = 3,122 (0.33%)
number of secondary alignments = 0
number of mapped bases = 48,861,356 bp
number of sequenced bases = 48,844,588 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 23,537
duplication rate = 2.05%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.7979
>>>>>>> ACTG content
number of A's = 11,657,436 bp (23.87%)
number of C's = 8,242,557 bp (16.88%)
number of T's = 16,636,205 bp (34.06%)
number of G's = 12,307,394 bp (25.2%)
number of N's = 996 bp (0%)
GC percentage = 42.07%
>>>>>>> Mismatches and indels
general error rate = 0.0052
number of mismatches = 250,364
number of insertions = 3,408
mapped reads with insertion percentage = 0.4%
number of deletions = 10,635
mapped reads with deletion percentage = 1.24%
homopolymer indels = 44.39%
>>>>>>> Coverage
mean coverageData = 0.0158X
std coverageData = 0.1785X
There is a 1.47% of reference with a coverageData >= 1X
There is a 0.07% of reference with a coverageData >= 2X
There is a 0.01% of reference with a coverageData >= 3X
There is a 0% of reference with a coverageData >= 4X
There is a 0% of reference with a coverageData >= 5X
There is a 0% of reference with a coverageData >= 6X
There is a 0% of reference with a coverageData >= 7X
There is a 0% of reference with a coverageData >= 8X
There is a 0% of reference with a coverageData >= 9X
There is a 0% of reference with a coverageData >= 10X
There is a 0% of reference with a coverageData >= 11X
There is a 0% of reference with a coverageData >= 12X
There is a 0% of reference with a coverageData >= 13X
There is a 0% of reference with a coverageData >= 14X
There is a 0% of reference with a coverageData >= 15X
There is a 0% of reference with a coverageData >= 16X
There is a 0% of reference with a coverageData >= 17X
There is a 0% of reference with a coverageData >= 18X
There is a 0% of reference with a coverageData >= 19X
There is a 0% of reference with a coverageData >= 20X
There is a 0% of reference with a coverageData >= 21X
There is a 0% of reference with a coverageData >= 22X
There is a 0% of reference with a coverageData >= 23X
There is a 0% of reference with a coverageData >= 24X
There is a 0% of reference with a coverageData >= 25X
There is a 0% of reference with a coverageData >= 26X
There is a 0% of reference with a coverageData >= 27X
There is a 0% of reference with a coverageData >= 28X
There is a 0% of reference with a coverageData >= 29X
There is a 0% of reference with a coverageData >= 30X
There is a 0% of reference with a coverageData >= 31X
There is a 0% of reference with a coverageData >= 32X
There is a 0% of reference with a coverageData >= 33X
There is a 0% of reference with a coverageData >= 34X
There is a 0% of reference with a coverageData >= 35X
There is a 0% of reference with a coverageData >= 36X
There is a 0% of reference with a coverageData >= 37X
There is a 0% of reference with a coverageData >= 38X
There is a 0% of reference with a coverageData >= 39X
There is a 0% of reference with a coverageData >= 40X
There is a 0% of reference with a coverageData >= 41X
There is a 0% of reference with a coverageData >= 42X
There is a 0% of reference with a coverageData >= 43X
There is a 0% of reference with a coverageData >= 44X
There is a 0% of reference with a coverageData >= 45X
There is a 0% of reference with a coverageData >= 46X
There is a 0% of reference with a coverageData >= 47X
There is a 0% of reference with a coverageData >= 48X
There is a 0% of reference with a coverageData >= 49X
There is a 0% of reference with a coverageData >= 50X
There is a 0% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 5542127 0.02223515824259471 0.29354178438200235
chr2 243199373 4034769 0.016590375831273218 0.22944880459000802
chr3 198022430 3635257 0.01835780421440137 0.14400159302806964
chr4 191154276 2806491 0.01468181125071981 0.13110606197220873
chr5 180915260 2214068 0.012238149507122837 0.11598215718249201
chr6 171115067 3060636 0.01788642025310372 0.1507206222934165
chr7 159138663 3565108 0.02240252577715825 0.28852962802715143
chr8 146364022 2821728 0.019278836160979505 0.2069944938570315
chr9 141213431 1588313 0.011247605760673006 0.13081756235370245
chr10 135534747 2541441 0.018751213664788116 0.17870092184267652
chr11 135006516 2188576 0.016210891628371478 0.15312615528707205
chr12 133851895 2171113 0.016220263448642247 0.13469420379432903
chr13 115169878 1529033 0.013276327339688594 0.12217982645643294
chr14 107349540 1814591 0.016903574994359547 0.13866714362235322
chr15 102531392 1299983 0.012678877899170627 0.12163369725184926
chr16 90354753 1262628 0.013974118218219245 0.1306917281077481
chr17 81195210 1089547 0.013418858082884446 0.12372251985381955
chr18 78077248 795534 0.010189063016155487 0.204757330694283
chr19 59128983 836180 0.014141626619892989 0.19326851229424002
chr20 63025520 845672 0.013417929752900095 0.12348935751177058
chr21 48129895 604020 0.012549788442297661 0.12125172784797086
chr22 51304566 404969 0.007893429992176525 0.09320516332114034
chrMT 16571 53781 3.2454891074769177 2.4986423950058216
chrX 155270560 2023582 0.013032618675426945 0.12762045038597053
chrY 59373566 132209 0.002226731673822657 0.06987857836971291