BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081181.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 = 1,971,368 number of mapped reads = 1,783,662 (90.48%) number of supplementary alignments = 15,567 (0.79%) number of secondary alignments = 0 number of mapped bases = 120,779,195 bp number of sequenced bases = 120,730,633 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,886 duplication rate = 2.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4549 >>>>>>> ACTG content number of A's = 34,306,179 bp (28.42%) number of C's = 22,482,691 bp (18.62%) number of T's = 37,818,392 bp (31.32%) number of G's = 26,087,150 bp (21.61%) number of N's = 36,221 bp (0.03%) GC percentage = 40.23% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,027,704 number of insertions = 9,771 mapped reads with insertion percentage = 0.54% number of deletions = 29,657 mapped reads with deletion percentage = 1.64% homopolymer indels = 46.37% >>>>>>> Coverage mean coverageData = 0.039X std coverageData = 0.3759X There is a 3.46% of reference with a coverageData >= 1X There is a 0.31% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 10659660 0.042766834269993656 0.7418547349947971 chr2 243199373 10023122 0.04121360131960537 0.41972829539928513 chr3 198022430 9201339 0.04646614527455299 0.23389346545567877 chr4 191154276 8509402 0.04451588621538343 0.23590878600699794 chr5 180915260 6689428 0.036975476806102484 0.21136648774710906 chr6 171115067 6906406 0.04036117988370948 0.3120100038888709 chr7 159138663 6579330 0.041343378635775016 0.47415915350939203 chr8 146364022 6947915 0.04747010163467631 0.47261188626289957 chr9 141213431 4307589 0.03050410268694626 0.33402195248543 chr10 135534747 4751464 0.035057165082545215 0.2890363001604409 chr11 135006516 5004329 0.037067314587986254 0.34070440066166324 chr12 133851895 4031804 0.03012138154637258 0.19559913869237783 chr13 115169878 3796228 0.032961986813948 0.19668630041299986 chr14 107349540 3782053 0.035231198941327556 0.22753104543096753 chr15 102531392 3948924 0.038514292286210255 0.2147045431929861 chr16 90354753 3486158 0.038583006253140886 0.24385782860727898 chr17 81195210 3413114 0.042035903349470986 0.27045006442270486 chr18 78077248 3566923 0.04568453795912479 0.6592859558352293 chr19 59128983 2380815 0.040264771677199315 0.5091734723288448 chr20 63025520 2508794 0.03980600239395089 0.2220670996145458 chr21 48129895 1770524 0.03678636739182581 0.224273123034283 chr22 51304566 1342673 0.026170633623525827 0.17473231942439227 chrMT 16571 78358 4.728622291955826 3.084326977284251 chrX 155270560 6788715 0.04372184269831963 0.2660285622764262 chrY 59373566 304128 0.005122279500611434 0.11386730387921891