BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506321.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 = 12,796,726 number of mapped reads = 10,140,860 (79.25%) number of supplementary alignments = 137,772 (1.08%) number of secondary alignments = 0 number of mapped bases = 796,054,569 bp number of sequenced bases = 795,722,711 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,154,263 duplication rate = 14.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.4984 >>>>>>> ACTG content number of A's = 212,296,939 bp (26.68%) number of C's = 146,672,049 bp (18.43%) number of T's = 235,775,834 bp (29.63%) number of G's = 200,802,204 bp (25.24%) number of N's = 175,685 bp (0.02%) GC percentage = 43.67% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 6,093,746 number of insertions = 63,159 mapped reads with insertion percentage = 0.61% number of deletions = 166,612 mapped reads with deletion percentage = 1.61% homopolymer indels = 43.73% >>>>>>> Coverage mean coverageData = 0.2571X std coverageData = 1.7278X There is a 12.38% of reference with a coverageData >= 1X There is a 5.65% of reference with a coverageData >= 2X There is a 2.93% of reference with a coverageData >= 3X There is a 1.62% of reference with a coverageData >= 4X There is a 0.93% of reference with a coverageData >= 5X There is a 0.56% of reference with a coverageData >= 6X There is a 0.35% of reference with a coverageData >= 7X There is a 0.23% of reference with a coverageData >= 8X There is a 0.15% of reference with a coverageData >= 9X There is a 0.11% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.06% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% 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% 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 58796952 0.23589490675732358 2.972320668561739 chr2 243199373 65910412 0.27101390594456837 1.9698195771687752 chr3 198022430 44402442 0.22422935624009865 0.8590317866035144 chr4 191154276 49396763 0.25841306840554273 1.4104710946404249 chr5 180915260 60781690 0.3359677342862067 1.0870238352872346 chr6 171115067 28370098 0.1657954410291643 0.8424569651335982 chr7 159138663 42033944 0.26413407783877135 2.3336462615653835 chr8 146364022 49454514 0.3378870935918938 2.3371417671616457 chr9 141213431 22136267 0.15675751834115553 1.8205411924724981 chr10 135534747 46270034 0.3413887215209838 1.981779826224789 chr11 135006516 35710999 0.2645131513504133 1.7071432247451215 chr12 133851895 34095752 0.2547274508142003 0.957725030865962 chr13 115169878 16975679 0.14739686535050422 0.6797917407512684 chr14 107349540 23259765 0.2166731687904764 1.1000595339928942 chr15 102531392 29554157 0.2882449601386471 1.0158106240749967 chr16 90354753 29830381 0.3301473360233744 1.3192233161515778 chr17 81195210 20711212 0.2550792343538492 1.1925910305888994 chr18 78077248 13820095 0.1770054062356296 2.5788414198649994 chr19 59128983 19669626 0.3326562542095473 2.2559324657596647 chr20 63025520 22319014 0.3541266141080629 1.198944181983598 chr21 48129895 13723114 0.2851266141345208 1.2952910997115914 chr22 51304566 9074030 0.176865934310798 0.8150320408139698 chrMT 16571 108720 6.5608593325689455 5.3908087650272885 chrX 155270560 56772543 0.36563623522707717 1.3898643865486349 chrY 59373566 2876366 0.04844522897614066 1.5815831904683786