BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716602.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 = 1,095,979
number of mapped reads = 965,925 (88.13%)
number of supplementary alignments = 4,721 (0.43%)
number of secondary alignments = 0
number of mapped bases = 55,100,591 bp
number of sequenced bases = 55,083,964 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 22,524
duplication rate = 1.58%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 42.9142
>>>>>>> ACTG content
number of A's = 14,342,696 bp (26.04%)
number of C's = 11,293,101 bp (20.5%)
number of T's = 16,744,132 bp (30.4%)
number of G's = 12,703,182 bp (23.06%)
number of N's = 853 bp (0%)
GC percentage = 43.56%
>>>>>>> Mismatches and indels
general error rate = 0.0052
number of mismatches = 280,879
number of insertions = 3,581
mapped reads with insertion percentage = 0.37%
number of deletions = 10,693
mapped reads with deletion percentage = 1.1%
homopolymer indels = 41.64%
>>>>>>> Coverage
mean coverageData = 0.0178X
std coverageData = 0.1991X
There is a 1.65% of reference with a coverageData >= 1X
There is a 0.09% 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 4491285 0.01801915269852026 0.23890603657771364
chr2 243199373 5434427 0.0223455633662345 0.23162505863424668
chr3 198022430 4157528 0.020995237761702045 0.16022793563307064
chr4 191154276 3163196 0.0165478694287749 0.13791777339972222
chr5 180915260 2847452 0.01573914770926455 0.13218189532088023
chr6 171115067 3164716 0.018494665931434312 0.15439410750588994
chr7 159138663 3200002 0.020108262440284547 0.4496174511015892
chr8 146364022 4412309 0.03014613113050419 0.20920404607955348
chr9 141213431 2240445 0.015865665072609135 0.15171564844508942
chr10 135534747 2652946 0.019573917823449364 0.2597477549248367
chr11 135006516 1868513 0.013840169018212424 0.14969450818205865
chr12 133851895 2596096 0.01939528760500552 0.15285930636666986
chr13 115169878 1477912 0.012832452596676364 0.11881526391929033
chr14 107349540 1406178 0.013099059390473402 0.12460665098078443
chr15 102531392 1282376 0.012507154881892172 0.11992136969637282
chr16 90354753 1605211 0.017765650911579604 0.14745214558556985
chr17 81195210 2139679 0.026352281125943268 0.17589866416553449
chr18 78077248 1275593 0.01633757634490396 0.2098725436150908
chr19 59128983 1039192 0.01757500209330507 0.22742898202134756
chr20 63025520 1164988 0.01848438537278233 0.14561926381309825
chr21 48129895 565896 0.011757681997851856 0.1167248957994493
chr22 51304566 716258 0.013960901647623333 0.12502046443980747
chrMT 16571 83915 5.063967171564782 4.246731757389213
chrX 155270560 1999128 0.012875125844847858 0.13497074299056114
chrY 59373566 115350 0.0019427837634007027 0.054269699534800424