BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524451.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 = 1,379,349
number of mapped reads = 1,281,508 (92.91%)
number of supplementary alignments = 3,831 (0.28%)
number of secondary alignments = 0
number of mapped bases = 77,714,248 bp
number of sequenced bases = 77,688,076 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 34,057
duplication rate = 1.9%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.0295
>>>>>>> ACTG content
number of A's = 21,687,947 bp (27.92%)
number of C's = 14,254,682 bp (18.35%)
number of T's = 23,421,683 bp (30.15%)
number of G's = 18,321,947 bp (23.58%)
number of N's = 1,817 bp (0%)
GC percentage = 41.93%
>>>>>>> Mismatches and indels
general error rate = 0.0048
number of mismatches = 354,235
number of insertions = 6,978
mapped reads with insertion percentage = 0.54%
number of deletions = 14,893
mapped reads with deletion percentage = 1.15%
homopolymer indels = 40.74%
>>>>>>> Coverage
mean coverageData = 0.0251X
std coverageData = 0.2394X
There is a 2.28% of reference with a coverageData >= 1X
There is a 0.16% of reference with a coverageData >= 2X
There is a 0.02% of reference with a coverageData >= 3X
There is a 0.01% 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 7616651 0.030558202701529077 0.4358238375318999
chr2 243199373 6157463 0.02531858089946638 0.2455053648978946
chr3 198022430 4274530 0.021586090020206297 0.1580841965248559
chr4 191154276 4481030 0.02344195533454873 0.182240275411546
chr5 180915260 4363432 0.02411865090871826 0.16650670460168535
chr6 171115067 3349936 0.019577095452383512 0.18406127885208323
chr7 159138663 3839941 0.024129529101297023 0.2976812711255538
chr8 146364022 7253245 0.04955620172831818 0.27320588251881545
chr9 141213431 3231763 0.022885663049996993 0.2153586769696459
chr10 135534747 4080753 0.030108537407016373 0.26322113907317946
chr11 135006516 2656085 0.01967375411717165 0.2081932624203834
chr12 133851895 3574623 0.026705807937945143 0.17628123692134545
chr13 115169878 1734355 0.015059102519844643 0.1308945047083718
chr14 107349540 1846548 0.017201266069700905 0.14414663451956566
chr15 102531392 2059683 0.02008831597643773 0.15470498870939714
chr16 90354753 2414700 0.026724659410003588 0.18654972839400127
chr17 81195210 2575937 0.03172523354518081 0.2008568682903681
chr18 78077248 1856237 0.02377436510057322 0.37224961196780754
chr19 59128983 1539181 0.026030906027928808 0.3286473152061965
chr20 63025520 2203274 0.03495844223102007 0.20418186686692122
chr21 48129895 1077973 0.022397160849821095 0.17138553083900016
chr22 51304566 600491 0.011704435819611066 0.1151551353283448
chrMT 16571 14695 0.8867901756079899 1.0203582346791331
chrX 155270560 4665965 0.03005054531908689 0.20058471616604398
chrY 59373566 245757 0.004139165230533736 0.12008698418838855