BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716857.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 = 634,337 number of mapped reads = 599,833 (94.56%) number of supplementary alignments = 13,454 (2.12%) number of secondary alignments = 0 number of mapped bases = 46,829,862 bp number of sequenced bases = 46,811,265 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,740 duplication rate = 1.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5067 >>>>>>> ACTG content number of A's = 12,027,970 bp (25.69%) number of C's = 9,920,940 bp (21.19%) number of T's = 13,676,769 bp (29.22%) number of G's = 11,183,909 bp (23.89%) number of N's = 1,677 bp (0%) GC percentage = 45.08% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 292,664 number of insertions = 4,549 mapped reads with insertion percentage = 0.74% number of deletions = 8,696 mapped reads with deletion percentage = 1.43% homopolymer indels = 38.17% >>>>>>> Coverage mean coverageData = 0.0151X std coverageData = 0.1648X There is a 1.39% 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 5162045 0.020710259333716965 0.2862005019549676 chr2 243199373 4437345 0.018245709046297583 0.17325814141144913 chr3 198022430 2967041 0.014983358198361671 0.13104068952482714 chr4 191154276 2297313 0.01201810939348278 0.14604207912557193 chr5 180915260 2810797 0.01553653904043252 0.13301783454943314 chr6 171115067 2899685 0.016945819271426285 0.1421672211408017 chr7 159138663 2925024 0.01838034796107342 0.19743939137066333 chr8 146364022 2917308 0.01993186549628979 0.17590148748767218 chr9 141213431 1380392 0.009775217486217723 0.1163652303205074 chr10 135534747 2499409 0.018441093928481676 0.22129002061406244 chr11 135006516 1388525 0.010284873953787535 0.12712868044995712 chr12 133851895 1674393 0.012509296188895944 0.11888426566902588 chr13 115169878 851128 0.007390196245584284 0.09015926642586765 chr14 107349540 895337 0.008340389721278731 0.09960448761073382 chr15 102531392 972794 0.009487767414686031 0.10284086095774213 chr16 90354753 1425360 0.015775152415058894 0.1373644409883432 chr17 81195210 846470 0.010425122368671748 0.11401338899847346 chr18 78077248 1380462 0.017680720509001546 0.18108117299950913 chr19 59128983 1173128 0.019840151825374706 0.21305818228722057 chr20 63025520 1253700 0.01989194218468963 0.1541661788016494 chr21 48129895 812254 0.016876288635161163 0.15309022342988796 chr22 51304566 727001 0.014170298214782676 0.12840907195984896 chrMT 16571 25498 1.5387122080743467 1.6325449193853834 chrX 155270560 2944235 0.01896196548785552 0.14918992120109573 chrY 59373566 163218 0.0027490011295599123 0.10836968206834319