BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695976.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 13,888,066 number of mapped reads = 12,637,194 (90.99%) number of supplementary alignments = 18,590 (0.13%) number of secondary alignments = 0 number of mapped bases = 1,709,616,150 bp number of sequenced bases = 1,698,127,355 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,911,593 duplication rate = 19.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 52.0222 >>>>>>> ACTG content number of A's = 464,465,093 bp (27.35%) number of C's = 381,643,111 bp (22.47%) number of T's = 464,944,043 bp (27.38%) number of G's = 387,075,108 bp (22.79%) number of N's = 0 bp (0%) GC percentage = 45.27% >>>>>>> Mismatches and indels general error rate = 0.0198 number of mismatches = 23,217,778 number of insertions = 9,593,523 mapped reads with insertion percentage = 45.97% number of deletions = 10,328,359 mapped reads with deletion percentage = 50.16% homopolymer indels = 36.68% >>>>>>> Coverage mean coverageData = 0.5523X std coverageData = 1.8967X There is a 18.57% of reference with a coverageData >= 1X There is a 10.8% of reference with a coverageData >= 2X There is a 6.86% of reference with a coverageData >= 3X There is a 4.61% of reference with a coverageData >= 4X There is a 3.23% of reference with a coverageData >= 5X There is a 2.34% of reference with a coverageData >= 6X There is a 1.73% of reference with a coverageData >= 7X There is a 1.31% of reference with a coverageData >= 8X There is a 1.01% of reference with a coverageData >= 9X There is a 0.78% of reference with a coverageData >= 10X There is a 0.62% of reference with a coverageData >= 11X There is a 0.49% of reference with a coverageData >= 12X There is a 0.39% of reference with a coverageData >= 13X There is a 0.32% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.22% of reference with a coverageData >= 16X There is a 0.18% of reference with a coverageData >= 17X There is a 0.15% of reference with a coverageData >= 18X There is a 0.12% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.09% of reference with a coverageData >= 21X There is a 0.08% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% 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 192987196 0.7742696697233103 2.5606292454291038 chr2 243199373 133785436 0.550106007057839 1.9215834231611588 chr3 198022430 116393581 0.5877797833306055 1.79425559279957 chr4 191154276 58410668 0.3055681997927161 1.3159031769054614 chr5 180915260 138281870 0.7643460811431827 2.33321853236729 chr6 171115067 80580712 0.47091535194852246 1.565815936278126 chr7 159138663 101712687 0.6391450391913874 1.9436091474032267 chr8 146364022 76919788 0.5255375395464331 1.7364313528805757 chr9 141213431 74094604 0.5246994104972919 1.8363873449460575 chr10 135534747 77377738 0.570907016191206 1.7989722442480343 chr11 135006516 96817427 0.7171315123782618 2.116643436361626 chr12 133851895 84015615 0.6276759473595798 1.9049366694399612 chr13 115169878 31670313 0.2749878140879857 1.1024477015695597 chr14 107349540 37275287 0.3472328526046781 1.2877553156429085 chr15 102531392 65171955 0.6356292812254026 2.007753650580906 chr16 90354753 71797491 0.7946177551943504 2.4301421616444387 chr17 81195210 49956035 0.6152584000952765 1.906873034013071 chr18 78077248 31323564 0.40118683486385176 1.6306290203353495 chr19 59128983 24243291 0.410006899662049 1.6091157877492455 chr20 63025520 61139243 0.9700712187697935 2.689764511302139 chr21 48129895 15043435 0.31255906542077433 2.225048496079949 chr22 51304566 20528175 0.4001237433720812 1.432775793196625 chrMT 16571 254906 15.382656448011586 17.36775091065796 chrX 155270560 67925802 0.4374673602001564 1.4690857629920724 chrY 59373566 1909331 0.03215793034900413 0.6520070949277869