BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549151.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 14,621,038 number of mapped reads = 12,749,863 (87.2%) number of secondary alignments = 0 number of mapped bases = 506,185,176 bp number of sequenced bases = 506,131,931 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 707,715 duplication rate = 4.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8512 >>>>>>> ACTG content number of A's = 147,983,662 bp (29.24%) number of C's = 104,347,206 bp (20.62%) number of T's = 149,512,796 bp (29.54%) number of G's = 104,185,965 bp (20.58%) number of N's = 102,302 bp (0.02%) GC percentage = 41.2% >>>>>>> Mismatches and indels general error rate = 0.0032 number of mismatches = 1,585,992 number of insertions = 12,412 mapped reads with insertion percentage = 0.1% number of deletions = 41,277 mapped reads with deletion percentage = 0.32% homopolymer indels = 45.23% >>>>>>> Coverage mean coverageData = 0.1635X std coverageData = 1.0091X There is a 11.52% of reference with a coverageData >= 1X There is a 3.2% of reference with a coverageData >= 2X There is a 0.94% of reference with a coverageData >= 3X There is a 0.29% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 40672206 0.16317795252353653 1.758660163480425 chr2 243199373 43161633 0.17747427745218736 0.8385305360332409 chr3 198022430 35102280 0.17726416143868146 0.5560603929068046 chr4 191154276 33288951 0.17414703817559382 0.6053293507005083 chr5 180915260 31850670 0.17605297640453327 0.5670013715162353 chr6 171115067 30280693 0.17696099782960667 0.6423214214035484 chr7 159138663 28429318 0.1786449468913786 1.432105807440416 chr8 146364022 26334711 0.17992612282819065 2.1389123827379106 chr9 141213431 21674943 0.15349066194702118 0.7816715375910481 chr10 135534747 24428919 0.18024100491366984 0.8800516923543915 chr11 135006516 23423847 0.1735016034337187 0.7679515412200087 chr12 133851895 23324538 0.1742563151608724 0.5894193117702273 chr13 115169878 16628234 0.1443800609044667 0.49210934043677645 chr14 107349540 16203188 0.15093858809269234 0.7054917689252863 chr15 102531392 15280667 0.14903403437651563 0.5029238775719995 chr16 90354753 14660323 0.1622529254216433 0.6068642590531694 chr17 81195210 13614086 0.1676710485754024 0.6015265900202871 chr18 78077248 13896018 0.17797781499675808 1.6349452628411065 chr19 59128983 9746556 0.16483550884005566 1.4745575076474393 chr20 63025520 10734809 0.17032479858952373 0.5997412877885427 chr21 48129895 6688774 0.1389733761106273 0.6040976400582834 chr22 51304566 5796373 0.11297967124407601 0.47905160478628595 chrMT 16571 61108 3.687647094321405 4.5957067135545575 chrX 155270560 16730860 0.10775294427997169 0.5822224196114372 chrY 59373566 4171471 0.07025805052706452 0.6247021133956167