BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013192.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,647,241 number of mapped reads = 2,143,157 (80.96%) number of supplementary alignments = 18,829 (0.71%) number of secondary alignments = 0 number of mapped bases = 138,998,228 bp number of sequenced bases = 138,930,791 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 207,607 duplication rate = 7.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1624 >>>>>>> ACTG content number of A's = 37,691,397 bp (27.13%) number of C's = 25,346,201 bp (18.24%) number of T's = 44,540,204 bp (32.06%) number of G's = 31,351,107 bp (22.57%) number of N's = 1,882 bp (0%) GC percentage = 40.81% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,063,236 number of insertions = 9,964 mapped reads with insertion percentage = 0.46% number of deletions = 38,571 mapped reads with deletion percentage = 1.78% homopolymer indels = 45.96% >>>>>>> Coverage mean coverageData = 0.0449X std coverageData = 0.5813X There is a 2.87% of reference with a coverageData >= 1X There is a 0.94% of reference with a coverageData >= 2X There is a 0.34% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.01% 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% 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 10152726 0.04073300182469756 1.3068770266718424 chr2 243199373 14024635 0.05766723337728342 0.5292640060072389 chr3 198022430 8327646 0.04205405417961996 0.3018153080598145 chr4 191154276 9356718 0.048948515281970466 0.3460813054662697 chr5 180915260 7454406 0.041203854224347906 0.2994445551017802 chr6 171115067 7245161 0.04234087112854884 0.37446028451423785 chr7 159138663 8754467 0.05501156560552479 1.0206705510110143 chr8 146364022 7340343 0.05015127966352277 0.6226603740181818 chr9 141213431 6160387 0.04362465352180275 0.3940485726760272 chr10 135534747 6113528 0.04510672086177281 0.4881330941628228 chr11 135006516 5688438 0.04213454408378333 0.36775553197438754 chr12 133851895 5848887 0.043696706722007934 0.30679832820101527 chr13 115169878 3769110 0.0327265259410972 0.2638944399654184 chr14 107349540 4184403 0.03897923549555964 0.31365176671645656 chr15 102531392 4623664 0.045095106091995706 0.31078859375617074 chr16 90354753 4203982 0.046527513610711765 0.33961616300885106 chr17 81195210 3648133 0.044930396756163324 0.364681491524896 chr18 78077248 2907086 0.037233458843221524 0.6681411092136761 chr19 59128983 3233678 0.054688544194984715 0.7807381930314994 chr20 63025520 3337748 0.052958674517877835 0.3462363823188469 chr21 48129895 1980919 0.041157766913890004 0.3145686285520043 chr22 51304566 1561303 0.03043204770507171 0.25090785717720465 chrMT 16571 52943 3.1949188341077788 2.8911355016320632 chrX 155270560 8665134 0.055806677067436354 0.40024381715917723 chrY 59373566 362783 0.006110177044107473 0.18002173173559274