BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081146.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,307,818 number of mapped reads = 2,026,037 (87.79%) number of supplementary alignments = 18,110 (0.78%) number of secondary alignments = 0 number of mapped bases = 134,315,426 bp number of sequenced bases = 134,268,331 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 84,833 duplication rate = 3.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6343 >>>>>>> ACTG content number of A's = 37,761,278 bp (28.12%) number of C's = 24,736,550 bp (18.42%) number of T's = 42,209,512 bp (31.44%) number of G's = 29,521,595 bp (21.99%) number of N's = 39,396 bp (0.03%) GC percentage = 40.41% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,119,446 number of insertions = 10,428 mapped reads with insertion percentage = 0.51% number of deletions = 29,305 mapped reads with deletion percentage = 1.43% homopolymer indels = 47.4% >>>>>>> Coverage mean coverageData = 0.0434X std coverageData = 0.3311X There is a 3.73% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% 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 10585477 0.0424692101368927 0.5033263701235127 chr2 243199373 11066774 0.04550494462006693 0.42155701690879366 chr3 198022430 9551942 0.04823666692707488 0.24676060500671188 chr4 191154276 9405591 0.04920418834889155 0.2581824440767936 chr5 180915260 8298716 0.04587073528236369 0.24209989152369807 chr6 171115067 7793255 0.045543943830498576 0.3161904442812426 chr7 159138663 7275947 0.04572080010500025 0.40079863750082945 chr8 146364022 6938044 0.04740266019746301 0.4171459432796404 chr9 141213431 6059368 0.042909289556175435 0.3252099374665966 chr10 135534747 6383661 0.04709981123881096 0.29296600116756655 chr11 135006516 6254317 0.04632603807063653 0.32733526069231184 chr12 133851895 5929796 0.04430117332294772 0.24239542643644735 chr13 115169878 4152727 0.03605740556571572 0.21351000045777188 chr14 107349540 4054110 0.03776550882286035 0.23236100089242806 chr15 102531392 3818264 0.03723995086304885 0.22264890667884216 chr16 90354753 3710199 0.04106257697367619 0.24732168286675377 chr17 81195210 3262220 0.040177493228972495 0.2702836349897407 chr18 78077248 3442325 0.04408870814709043 0.5434492440907 chr19 59128983 2198965 0.037189291755618394 0.39598493320216793 chr20 63025520 2608822 0.041393105522969105 0.2336925911458691 chr21 48129895 1790113 0.037193370149675165 0.23035811328295938 chr22 51304566 1381235 0.026922262630581457 0.18374431878121794 chrMT 16571 3745 0.22599722406613965 0.5320368469927448 chrX 155270560 8035039 0.05174863154998604 0.27798065497704677 chrY 59373566 314774 0.005301584883751129 0.11036810076895485