BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716601.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 = 1,360,915 number of mapped reads = 1,149,384 (84.46%) number of supplementary alignments = 6,385 (0.47%) number of secondary alignments = 0 number of mapped bases = 66,521,438 bp number of sequenced bases = 66,502,441 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 35,697 duplication rate = 2.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7626 >>>>>>> ACTG content number of A's = 16,810,419 bp (25.28%) number of C's = 12,728,471 bp (19.14%) number of T's = 21,059,818 bp (31.67%) number of G's = 15,902,920 bp (23.91%) number of N's = 813 bp (0%) GC percentage = 43.05% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 327,179 number of insertions = 5,363 mapped reads with insertion percentage = 0.47% number of deletions = 12,022 mapped reads with deletion percentage = 1.04% homopolymer indels = 41.51% >>>>>>> Coverage mean coverageData = 0.0215X std coverageData = 0.2028X There is a 1.97% of reference with a coverageData >= 1X There is a 0.13% of reference with a coverageData >= 2X There is a 0.02% 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 5361802 0.021511689633864545 0.3000568431519778 chr2 243199373 5644816 0.023210651945225202 0.2788153621890279 chr3 198022430 4312894 0.021779825649043898 0.15836635107878294 chr4 191154276 4194684 0.021943971580316624 0.17058554720228106 chr5 180915260 4042920 0.02234703694978522 0.16033491258360316 chr6 171115067 3803207 0.022226020575967165 0.17210618263656127 chr7 159138663 3673780 0.02308540194283271 0.2689106719585563 chr8 146364022 3381388 0.02310259006137451 0.19389271595326535 chr9 141213431 2700552 0.01912390330633635 0.1700264646580556 chr10 135534747 3133462 0.023119252216555215 0.20269385690452438 chr11 135006516 2913103 0.021577499266776132 0.18726405744899494 chr12 133851895 3036292 0.022683967231095233 0.16303943666184417 chr13 115169878 2030976 0.017634611022163276 0.14321616534037146 chr14 107349540 2071950 0.019300967661342563 0.15461467553551403 chr15 102531392 1961404 0.019129790025673308 0.15474993778645252 chr16 90354753 2017411 0.022327668805646562 0.1662164455080997 chr17 81195210 1911780 0.023545477621155237 0.1726274802030779 chr18 78077248 1747836 0.022385983686310257 0.26768677680219427 chr19 59128983 1435048 0.024269789994527727 0.24336710865358943 chr20 63025520 1466269 0.023264687066445466 0.1655294025170788 chr21 48129895 883768 0.01836214269738174 0.15756966459571936 chr22 51304566 858338 0.016730245803073356 0.13945261028283218 chrMT 16571 7447 0.44939955343672683 0.7284125538210884 chrX 155270560 3734395 0.024050888977279403 0.17803706797507063 chrY 59373566 195916 0.0032997175881266756 0.08828170164754717