BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717031.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 = 807,385 number of mapped reads = 738,063 (91.41%) number of supplementary alignments = 3,657 (0.45%) number of secondary alignments = 0 number of mapped bases = 43,016,464 bp number of sequenced bases = 43,003,174 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,530 duplication rate = 1.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3596 >>>>>>> ACTG content number of A's = 10,426,205 bp (24.25%) number of C's = 8,255,480 bp (19.2%) number of T's = 13,582,201 bp (31.58%) number of G's = 10,738,792 bp (24.97%) number of N's = 496 bp (0%) GC percentage = 44.17% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 219,709 number of insertions = 2,854 mapped reads with insertion percentage = 0.38% number of deletions = 8,330 mapped reads with deletion percentage = 1.12% homopolymer indels = 42.69% >>>>>>> Coverage mean coverageData = 0.0139X std coverageData = 0.1605X There is a 1.31% of reference with a coverageData >= 1X There is a 0.05% 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 3594337 0.014420573900997422 0.2083590328417331 chr2 243199373 4287788 0.01763075269112639 0.1796367659894418 chr3 198022430 3342384 0.01687881519280417 0.1396552937541542 chr4 191154276 2462720 0.012883415697172267 0.12004141040013272 chr5 180915260 2177548 0.0120362870440006 0.11404914232464604 chr6 171115067 2443579 0.014280326349052594 0.12975642285558944 chr7 159138663 2709052 0.01702321704185739 0.31989462837878835 chr8 146364022 3059236 0.020901557351300445 0.1745351563296629 chr9 141213431 1544923 0.010940340370315058 0.12115605324032808 chr10 135534747 2048442 0.015113777428602865 0.20472988466034436 chr11 135006516 1284917 0.009517444328390787 0.11646620473237833 chr12 133851895 2005105 0.014980026991773258 0.13485953441882154 chr13 115169878 1145863 0.00994932893824894 0.10361145068513475 chr14 107349540 1098502 0.010232945572007109 0.10726855342083917 chr15 102531392 1036206 0.010106231660250941 0.10583816359071439 chr16 90354753 1330775 0.01472833421391789 0.12957698982139748 chr17 81195210 1814847 0.022351651039513292 0.15874345413499832 chr18 78077248 1032945 0.013229782381674108 0.18093456737760913 chr19 59128983 873716 0.014776442206015957 0.18924250758396888 chr20 63025520 972459 0.015429606927479536 0.13279902831371995 chr21 48129895 441318 0.009169311505873844 0.1003518197610014 chr22 51304566 653404 0.01273578651849428 0.1174492674849189 chrMT 16571 44863 2.707320016896989 2.123809115940277 chrX 155270560 1520157 0.009790374942938313 0.1119168412863296 chrY 59373566 91378 0.001539035064863714 0.04636343990132787