BamQC report ----------------------------------- >>>>>>> Input bam file = SRR053635.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 13,269,824 number of mapped reads = 9,924,272 (74.79%) number of supplementary alignments = 257 (0%) number of secondary alignments = 0 number of mapped bases = 465,115,121 bp number of sequenced bases = 465,021,204 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,247,350 duplication rate = 20.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1008 >>>>>>> ACTG content number of A's = 143,139,948 bp (30.78%) number of C's = 90,485,429 bp (19.46%) number of T's = 138,023,884 bp (29.68%) number of G's = 93,369,253 bp (20.08%) number of N's = 2,690 bp (0%) GC percentage = 39.54% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 2,590,422 number of insertions = 20,671 mapped reads with insertion percentage = 0.21% number of deletions = 64,285 mapped reads with deletion percentage = 0.65% homopolymer indels = 46.98% >>>>>>> Coverage mean coverageData = 0.1502X std coverageData = 1.3187X There is a 5.13% of reference with a coverageData >= 1X There is a 2.26% of reference with a coverageData >= 2X There is a 1.44% of reference with a coverageData >= 3X There is a 1.04% of reference with a coverageData >= 4X There is a 0.79% of reference with a coverageData >= 5X There is a 0.62% of reference with a coverageData >= 6X There is a 0.5% of reference with a coverageData >= 7X There is a 0.41% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.28% of reference with a coverageData >= 10X There is a 0.24% of reference with a coverageData >= 11X There is a 0.21% of reference with a coverageData >= 12X There is a 0.18% of reference with a coverageData >= 13X There is a 0.15% of reference with a coverageData >= 14X There is a 0.13% of reference with a coverageData >= 15X There is a 0.12% of reference with a coverageData >= 16X There is a 0.1% of reference with a coverageData >= 17X There is a 0.09% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% 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 0.03% of reference with a coverageData >= 30X There is a 0.03% 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 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% 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 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 36205076 0.14525571031576287 1.3547715467420929 chr2 243199373 39357236 0.1618311573525315 1.4472050579257805 chr3 198022430 32351280 0.1633717958112119 1.3138762268824522 chr4 191154276 31700937 0.16583953894915748 1.3726370858152757 chr5 180915260 29313479 0.1620287807673051 1.2861692409114638 chr6 171115067 27501618 0.16072002589929735 1.36705707094158 chr7 159138663 25282202 0.15886901098320777 1.4385090894792114 chr8 146364022 23783526 0.16249571223179424 1.4358919903132963 chr9 141213431 19086956 0.13516388536724952 1.2187070930292052 chr10 135534747 21168773 0.15618705511731246 1.3352325388293917 chr11 135006516 20854514 0.15447042570893393 1.397864406232347 chr12 133851895 21153956 0.15804001878344717 1.2792551708367952 chr13 115169878 15783412 0.13704461855902983 1.2042973449504562 chr14 107349540 14541459 0.13545897821266864 1.307964575832621 chr15 102531392 12920473 0.12601480139858046 1.1144746195041126 chr16 90354753 12817604 0.14185865795018 1.2217913165631384 chr17 81195210 11642711 0.14339159908570961 1.1818846198555057 chr18 78077248 12310823 0.15767490934106693 1.4263100184989153 chr19 59128983 7866584 0.13304108409914644 1.2590472410429943 chr20 63025520 9321298 0.14789720100683024 1.2449980512721517 chr21 48129895 6140008 0.12757160596340383 1.1909870363559576 chr22 51304566 4754141 0.09266506610737142 0.9289638425067749 chrMT 16571 103829 6.265705147546919 15.375456133986956 chrX 155270560 27985319 0.1802358347905746 1.4480932275419411 chrY 59373566 1167907 0.019670487704915685 0.38720518040466045