BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234067.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 6,293,109 number of mapped reads = 5,919,797 (94.07%) number of supplementary alignments = 36,587 (0.58%) number of secondary alignments = 0 number of mapped bases = 402,665,113 bp number of sequenced bases = 402,526,217 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 505,506 duplication rate = 3.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.9812 >>>>>>> ACTG content number of A's = 108,708,475 bp (27.01%) number of C's = 75,249,020 bp (18.69%) number of T's = 117,198,700 bp (29.12%) number of G's = 101,281,449 bp (25.16%) number of N's = 88,573 bp (0.02%) GC percentage = 43.86% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 2,620,736 number of insertions = 27,438 mapped reads with insertion percentage = 0.46% number of deletions = 86,645 mapped reads with deletion percentage = 1.45% homopolymer indels = 46.14% >>>>>>> Coverage mean coverageData = 0.1301X std coverageData = 28.6471X There is a 8.87% of reference with a coverageData >= 1X There is a 2.3% of reference with a coverageData >= 2X There is a 0.7% of reference with a coverageData >= 3X There is a 0.25% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 40836811 0.16383835208177877 1.621063488791378 chr2 243199373 45284573 0.18620349403614622 102.15941431236342 chr3 198022430 10372922 0.05238256090484295 0.30894205085958876 chr4 191154276 23515170 0.1230167092887841 0.48377698624762455 chr5 180915260 20297818 0.11219516805823898 0.4467160373744281 chr6 171115067 14307413 0.08361281826807221 0.438409620253567 chr7 159138663 23025518 0.1446883966845945 0.9887663638486365 chr8 146364022 34596905 0.23637574676651069 1.3738400259486594 chr9 141213431 13134020 0.0930082918245928 0.9728075574773305 chr10 135534747 23664235 0.17459902736233388 0.806889434351979 chr11 135006516 7775031 0.057590042542835486 0.7081858445095021 chr12 133851895 12386148 0.09253621698818683 0.43252639781375235 chr13 115169878 24130715 0.20952279727169634 0.6259805984973466 chr14 107349540 19578690 0.18238261663720218 0.8270804889883423 chr15 102531392 10442629 0.10184811496560975 0.42723338063278327 chr16 90354753 12422681 0.1374878530186453 0.6554695304385558 chr17 81195210 5928123 0.07301074780150209 0.506406801279841 chr18 78077248 13018528 0.1667390735902987 2.2118452927508128 chr19 59128983 3262798 0.05518102687475616 1.223782015837775 chr20 63025520 11591516 0.18391781614812538 0.6606604814314508 chr21 48129895 9048997 0.18801198298895105 0.679434156119067 chr22 51304566 667643 0.013013325168757884 0.14837117284752757 chrMT 16571 30931 1.8665741355379881 2.1521435016393857 chrX 155270560 22399462 0.14426084378133242 0.652761184490485 chrY 59373566 945836 0.015930254214476525 0.23216926699060547