BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716542.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 = 450,011 number of mapped reads = 410,552 (91.23%) number of supplementary alignments = 1,477 (0.33%) number of secondary alignments = 0 number of mapped bases = 23,835,749 bp number of sequenced bases = 23,828,608 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,308 duplication rate = 1.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3546 >>>>>>> ACTG content number of A's = 5,931,945 bp (24.89%) number of C's = 4,659,819 bp (19.56%) number of T's = 7,480,352 bp (31.39%) number of G's = 5,755,681 bp (24.15%) number of N's = 811 bp (0%) GC percentage = 43.71% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 121,094 number of insertions = 1,686 mapped reads with insertion percentage = 0.41% number of deletions = 4,553 mapped reads with deletion percentage = 1.1% homopolymer indels = 43.53% >>>>>>> Coverage mean coverageData = 0.0077X std coverageData = 0.1067X There is a 0.73% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0% 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 1933001 0.00775525048742005 0.16832882950341788 chr2 243199373 2027626 0.008337299455126474 0.12176393571305022 chr3 198022430 1585023 0.008004259921464453 0.09240107855251907 chr4 191154276 1536788 0.008039516730454934 0.09501478977819154 chr5 180915260 1441217 0.007966254477372444 0.0922638869002336 chr6 171115067 1367052 0.007989080236867745 0.09730806180629831 chr7 159138663 1311637 0.008242101418182707 0.1136256766572622 chr8 146364022 1202324 0.008214614381121612 0.10947942928077176 chr9 141213431 972944 0.006889882875234439 0.09430268782893411 chr10 135534747 1148246 0.008471967708767701 0.10650302563041354 chr11 135006516 1097317 0.008127881768314056 0.09962982138658572 chr12 133851895 1073061 0.00801677854467432 0.09300164871108231 chr13 115169878 737753 0.006405780858776285 0.08293406486544841 chr14 107349540 728566 0.006786857214292674 0.08566238748882074 chr15 102531392 686665 0.006697119648975409 0.08514597319279447 chr16 90354753 669597 0.007410755690959611 0.09092349035049804 chr17 81195210 655552 0.008073776765895426 0.09437851015239586 chr18 78077248 625444 0.008010579471243659 0.1289325638792546 chr19 59128983 492764 0.008333713434577422 0.12577622128265742 chr20 63025520 499857 0.007931025400504431 0.09283694021805834 chr21 48129895 317753 0.006601988223743268 0.08641601742340653 chr22 51304566 280734 0.005471910628773276 0.07658260748572834 chrMT 16571 7743 0.4672620843642508 0.7262803906880831 chrX 155270560 1359033 0.008752676618156076 0.09916764320407462 chrY 59373566 78052 0.0013145917494664207 0.04894593001018632