BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153352.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 36,492,040 number of mapped reads = 36,250,522 (99.34%) number of supplementary alignments = 239,887 (0.66%) number of secondary alignments = 0 number of mapped bases = 3,133,439,636 bp number of sequenced bases = 3,132,933,347 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,104,103 duplication rate = 46.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.8998 >>>>>>> ACTG content number of A's = 829,767,322 bp (26.49%) number of C's = 743,029,531 bp (23.72%) number of T's = 855,862,361 bp (27.32%) number of G's = 703,389,341 bp (22.45%) number of N's = 884,792 bp (0.03%) GC percentage = 46.17% >>>>>>> Mismatches and indels general error rate = 0.0023 number of mismatches = 6,857,446 number of insertions = 323,773 mapped reads with insertion percentage = 0.88% number of deletions = 248,645 mapped reads with deletion percentage = 0.68% homopolymer indels = 48.95% >>>>>>> Coverage mean coverageData = 1.0122X std coverageData = 11.963X There is a 11.35% of reference with a coverageData >= 1X There is a 7.97% of reference with a coverageData >= 2X There is a 3.4% of reference with a coverageData >= 3X There is a 2.8% of reference with a coverageData >= 4X There is a 2.01% of reference with a coverageData >= 5X There is a 1.8% of reference with a coverageData >= 6X There is a 1.6% of reference with a coverageData >= 7X There is a 1.49% of reference with a coverageData >= 8X There is a 1.4% of reference with a coverageData >= 9X There is a 1.33% of reference with a coverageData >= 10X There is a 1.26% of reference with a coverageData >= 11X There is a 1.21% of reference with a coverageData >= 12X There is a 1.16% of reference with a coverageData >= 13X There is a 1.12% of reference with a coverageData >= 14X There is a 1.08% of reference with a coverageData >= 15X There is a 1.04% of reference with a coverageData >= 16X There is a 1.01% of reference with a coverageData >= 17X There is a 0.97% of reference with a coverageData >= 18X There is a 0.94% of reference with a coverageData >= 19X There is a 0.92% of reference with a coverageData >= 20X There is a 0.89% of reference with a coverageData >= 21X There is a 0.87% of reference with a coverageData >= 22X There is a 0.84% of reference with a coverageData >= 23X There is a 0.82% of reference with a coverageData >= 24X There is a 0.8% of reference with a coverageData >= 25X There is a 0.78% of reference with a coverageData >= 26X There is a 0.76% of reference with a coverageData >= 27X There is a 0.74% of reference with a coverageData >= 28X There is a 0.72% of reference with a coverageData >= 29X There is a 0.7% of reference with a coverageData >= 30X There is a 0.69% of reference with a coverageData >= 31X There is a 0.67% of reference with a coverageData >= 32X There is a 0.65% of reference with a coverageData >= 33X There is a 0.64% of reference with a coverageData >= 34X There is a 0.63% of reference with a coverageData >= 35X There is a 0.61% of reference with a coverageData >= 36X There is a 0.6% of reference with a coverageData >= 37X There is a 0.59% of reference with a coverageData >= 38X There is a 0.57% of reference with a coverageData >= 39X There is a 0.56% of reference with a coverageData >= 40X There is a 0.55% of reference with a coverageData >= 41X There is a 0.54% of reference with a coverageData >= 42X There is a 0.53% of reference with a coverageData >= 43X There is a 0.52% of reference with a coverageData >= 44X There is a 0.51% of reference with a coverageData >= 45X There is a 0.5% of reference with a coverageData >= 46X There is a 0.49% of reference with a coverageData >= 47X There is a 0.48% of reference with a coverageData >= 48X There is a 0.47% of reference with a coverageData >= 49X There is a 0.46% of reference with a coverageData >= 50X There is a 0.45% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 331377186 1.3294939233070155 15.369472241313783 chr2 243199373 245395405 1.0090297601219556 11.426202577396905 chr3 198022430 173019007 0.8737343895840486 10.087684410677253 chr4 191154276 129673467 0.678370736524879 8.608124418991654 chr5 180915260 188868638 1.0439618968571254 11.593836156059716 chr6 171115067 111014793 0.6487727524309709 8.329835987189853 chr7 159138663 143564289 0.902133311249448 10.841572470973226 chr8 146364022 187699986 1.2824188857012961 15.503171452107425 chr9 141213431 81423919 0.5766018035494088 7.746711605423143 chr10 135534747 164607693 1.2145054802810087 12.933638645412666 chr11 135006516 144212461 1.0681888939345712 12.29835922654134 chr12 133851895 165323065 1.2351193459009302 12.957899476418907 chr13 115169878 39873171 0.3462118020130229 4.78145997706924 chr14 107349540 92658438 0.8631470428285021 9.562541442933657 chr15 102531392 141333626 1.378442477402433 13.785568057612924 chr16 90354753 142829090 1.5807590110948564 16.876281780346055 chr17 81195210 124977218 1.5392190992547468 13.92967690381661 chr18 78077248 39265098 0.5029006401455133 6.968673401935949 chr19 59128983 158477747 2.6802041733070228 22.87438826918156 chr20 63025520 82817843 1.3140366473771259 14.33473327814553 chr21 48129895 31895051 0.6626869017686409 8.602573857121472 chr22 51304566 46172297 0.8999646737095486 10.63561079943876 chrMT 16571 4634 0.27964516323698024 0.8867473941405276 chrX 155270560 164833925 1.0615916178830036 12.119933562437348 chrY 59373566 2121589 0.035732888268829935 1.8335092488197489