BamQC report ----------------------------------- >>>>>>> Input bam file = SRR090133.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 = 18,722,724 number of mapped reads = 15,788,572 (84.33%) number of supplementary alignments = 833 (0%) number of secondary alignments = 0 number of mapped bases = 739,200,345 bp number of sequenced bases = 739,050,462 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,500,475 duplication rate = 10.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6861 >>>>>>> ACTG content number of A's = 233,682,042 bp (31.62%) number of C's = 145,153,545 bp (19.64%) number of T's = 204,845,743 bp (27.72%) number of G's = 155,343,824 bp (21.02%) number of N's = 25,308 bp (0%) GC percentage = 40.66% >>>>>>> Mismatches and indels general error rate = 0.0041 number of mismatches = 3,016,995 number of insertions = 32,246 mapped reads with insertion percentage = 0.2% number of deletions = 100,310 mapped reads with deletion percentage = 0.63% homopolymer indels = 45.96% >>>>>>> Coverage mean coverageData = 0.2388X std coverageData = 1.528X There is a 12.28% of reference with a coverageData >= 1X There is a 4.31% of reference with a coverageData >= 2X There is a 2.04% of reference with a coverageData >= 3X There is a 1.17% of reference with a coverageData >= 4X There is a 0.77% of reference with a coverageData >= 5X There is a 0.55% of reference with a coverageData >= 6X There is a 0.41% of reference with a coverageData >= 7X There is a 0.32% of reference with a coverageData >= 8X There is a 0.25% of reference with a coverageData >= 9X There is a 0.21% of reference with a coverageData >= 10X There is a 0.17% of reference with a coverageData >= 11X There is a 0.14% of reference with a coverageData >= 12X There is a 0.12% of reference with a coverageData >= 13X There is a 0.1% of reference with a coverageData >= 14X There is a 0.09% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% 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 0.01% of reference with a coverageData >= 32X There is a 0.01% 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 0.01% 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% 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 59610454 0.23915869802386572 1.6451270138018912 chr2 243199373 77575282 0.31897813322076285 1.655975801054388 chr3 198022430 65236601 0.3294404628808969 1.4503419568704505 chr4 191154276 39150133 0.20480908834077036 0.99355305616526 chr5 180915260 34649116 0.19152124591369463 0.9473197266458632 chr6 171115067 41972719 0.24528944023380478 1.1984925237301896 chr7 159138663 54250003 0.3408976924733872 2.3237405998791574 chr8 146364022 65983059 0.45081474325705534 3.791105344564496 chr9 141213431 23717552 0.16795535546473622 1.1348416903925582 chr10 135534747 22384994 0.16516055473213817 1.0151478894404113 chr11 135006516 30622387 0.226821548376228 1.2154317141068949 chr12 133851895 27378315 0.2045418557578135 0.9934864189215336 chr13 115169878 23398482 0.20316494561190732 0.9984210974356882 chr14 107349540 26633567 0.24810136121682497 1.183574544076558 chr15 102531392 19823400 0.1933398114793955 0.9901957246739959 chr16 90354753 14711637 0.16282084241877126 0.9048148606732888 chr17 81195210 14863342 0.18305688229638176 0.9534985670601696 chr18 78077248 26203028 0.33560388808785885 1.778339761470262 chr19 59128983 11103613 0.18778630100910074 1.378794941707 chr20 63025520 17306867 0.2746009394289805 1.2366291851856608 chr21 48129895 9878903 0.2052550291248298 1.1062228438054011 chr22 51304566 5869467 0.11440437874476904 0.7096058277996408 chrMT 16571 401601 24.235169875082978 25.797335918033646 chrX 155270560 24829693 0.15991243285269274 0.9166510592334868 chrY 59373566 1646130 0.02772496433850714 0.7259208500291429