BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068962.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 = 2,024,988 number of mapped reads = 1,652,951 (81.63%) number of supplementary alignments = 5,375 (0.27%) number of secondary alignments = 0 number of mapped bases = 102,868,795 bp number of sequenced bases = 102,815,530 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 128,194 duplication rate = 6.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3239 >>>>>>> ACTG content number of A's = 26,783,372 bp (26.05%) number of C's = 16,699,967 bp (16.24%) number of T's = 35,103,640 bp (34.14%) number of G's = 23,991,539 bp (23.33%) number of N's = 237,012 bp (0.23%) GC percentage = 39.58% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 1,002,861 number of insertions = 8,301 mapped reads with insertion percentage = 0.5% number of deletions = 34,324 mapped reads with deletion percentage = 2.05% homopolymer indels = 49.79% >>>>>>> Coverage mean coverageData = 0.0332X std coverageData = 0.3097X There is a 2.59% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 12274796 0.04924680207717517 0.4464220537341719 chr2 243199373 8682665 0.035701839576699895 0.2918538196413734 chr3 198022430 5342272 0.026978115559939345 0.20646113508084704 chr4 191154276 6539337 0.03420973434044447 0.24157826309006253 chr5 180915260 6694598 0.03700405372106256 0.24066130074926115 chr6 171115067 6983980 0.04081452394837913 0.3414157760100175 chr7 159138663 7669600 0.04819444788222206 0.5870305702650216 chr8 146364022 7885054 0.05387289780817857 0.4418261224556888 chr9 141213431 4020726 0.028472688267166316 0.2935933713053209 chr10 135534747 3903776 0.028802768931276347 0.27399424016592927 chr11 135006516 3746320 0.027749179158137818 0.2353319115150022 chr12 133851895 4352289 0.032515707005866444 0.2307209616468475 chr13 115169878 2147861 0.01864950312789252 0.17185735565180016 chr14 107349540 3551171 0.0330804491570248 0.23111993559725344 chr15 102531392 2262574 0.022067134327016645 0.18612458919841424 chr16 90354753 1959859 0.021690712828355583 0.1908851782300114 chr17 81195210 2066630 0.025452609827599434 0.22150495693039227 chr18 78077248 1602024 0.02051844860105725 0.3678896050846769 chr19 59128983 1222627 0.02067728782008647 0.3220659698317694 chr20 63025520 1621652 0.025730085209927662 0.20465224654011677 chr21 48129895 1118600 0.023241272394215695 0.1980001968007471 chr22 51304566 836743 0.016309328101518295 0.15670952405253633 chrMT 16571 114437 6.905859634300887 5.154801098091026 chrX 155270560 6050578 0.038967966625482645 0.2737327131700433 chrY 59373566 218626 0.0036822110364737063 0.09011364222511024