BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10525085.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 = 1,390,080
number of mapped reads = 1,289,001 (92.73%)
number of supplementary alignments = 5,233 (0.38%)
number of secondary alignments = 0
number of mapped bases = 76,251,542 bp
number of sequenced bases = 76,227,631 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 104,571
duplication rate = 6.41%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.294
>>>>>>> ACTG content
number of A's = 18,582,085 bp (24.38%)
number of C's = 15,055,289 bp (19.75%)
number of T's = 23,593,551 bp (30.95%)
number of G's = 18,988,981 bp (24.91%)
number of N's = 7,725 bp (0.01%)
GC percentage = 44.66%
>>>>>>> Mismatches and indels
general error rate = 0.005
number of mismatches = 368,943
number of insertions = 4,964
mapped reads with insertion percentage = 0.38%
number of deletions = 14,443
mapped reads with deletion percentage = 1.11%
homopolymer indels = 43.71%
>>>>>>> Coverage
mean coverageData = 0.0246X
std coverageData = 0.2671X
There is a 2.05% of reference with a coverageData >= 1X
There is a 0.3% of reference with a coverageData >= 2X
There is a 0.06% of reference with a coverageData >= 3X
There is a 0.01% of reference with a coverageData >= 4X
There is a 0.01% 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 6275946 0.025179259232417317 0.4667813522750166
chr2 243199373 6574040 0.027031484164229323 0.314377200939052
chr3 198022430 4976551 0.02513124902062862 0.18344254726696899
chr4 191154276 5120407 0.026786777189331618 0.2625139002250609
chr5 180915260 4707720 0.02602168551176943 0.18827882798398313
chr6 171115067 4365721 0.025513364056947714 0.19890035250923294
chr7 159138663 4132198 0.025966021845992258 0.2843552844587378
chr8 146364022 3961194 0.027063987077370694 0.33205092026183014
chr9 141213431 3300780 0.023374405512461487 0.21462737290764
chr10 135534747 3935374 0.02903590471895742 0.3427048634129124
chr11 135006516 3549645 0.02629239762027486 0.2171688487833368
chr12 133851895 3455161 0.025813314036383272 0.19191241169078377
chr13 115169878 2428206 0.02108368995580598 0.1692687242721243
chr14 107349540 2361906 0.02200201323638648 0.17622150922007881
chr15 102531392 2334979 0.02277330829566812 0.17377995587482614
chr16 90354753 2321833 0.025696855150497726 0.1997762527278511
chr17 81195210 2165379 0.026668802260625967 0.20339617708457233
chr18 78077248 2087985 0.02674255373345126 0.34471357919990925
chr19 59128983 1628390 0.027539624687947024 0.3317571571432083
chr20 63025520 1729435 0.02744023373389065 0.20449472453630815
chr21 48129895 1076039 0.022356977924011676 0.24036207476560376
chr22 51304566 1013214 0.019749002457208193 0.16556382197365815
chrMT 16571 30085 1.8155210910627 1.7477033412592569
chrX 155270560 2408751 0.015513249903909666 0.15726980863918916
chrY 59373566 310603 0.005231334766047234 0.24362714380643238