BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237322.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 = 3,335,862 number of mapped reads = 3,003,176 (90.03%) number of supplementary alignments = 29,756 (0.89%) number of secondary alignments = 0 number of mapped bases = 181,586,476 bp number of sequenced bases = 181,495,046 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 641,002 duplication rate = 17.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4994 >>>>>>> ACTG content number of A's = 45,326,124 bp (24.97%) number of C's = 31,538,374 bp (17.38%) number of T's = 60,766,998 bp (33.48%) number of G's = 43,844,961 bp (24.16%) number of N's = 18,589 bp (0.01%) GC percentage = 41.53% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 1,106,375 number of insertions = 12,111 mapped reads with insertion percentage = 0.4% number of deletions = 53,011 mapped reads with deletion percentage = 1.74% homopolymer indels = 41.86% >>>>>>> Coverage mean coverageData = 0.0587X std coverageData = 0.7432X There is a 3.49% of reference with a coverageData >= 1X There is a 1.29% of reference with a coverageData >= 2X There is a 0.53% of reference with a coverageData >= 3X There is a 0.23% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.05% 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% 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 14249743 0.057170341011908654 0.9514714485510212 chr2 243199373 17426518 0.07165527519678268 1.6886160848598775 chr3 198022430 10779305 0.054434767818978894 0.3647597856606713 chr4 191154276 11995109 0.06275093213190795 0.43896264870114526 chr5 180915260 10863782 0.06004900858003907 0.38561050220826293 chr6 171115067 9738721 0.05691328747806878 0.6292559460625502 chr7 159138663 12390292 0.07785846485338387 0.7689748772394315 chr8 146364022 10730350 0.07331275714738147 0.8231464616094993 chr9 141213431 8625069 0.06107824828645372 0.47224501896808224 chr10 135534747 7579697 0.05592438225453728 0.5720931603755172 chr11 135006516 8360246 0.06192475924643519 0.44304967586515037 chr12 133851895 8073512 0.06031675532124517 0.3855643085510626 chr13 115169878 5177334 0.044953889766211265 0.40728567189340986 chr14 107349540 5723288 0.05331450884652137 0.3743822879224887 chr15 102531392 4736874 0.046199255736233444 0.39600197748783733 chr16 90354753 4378370 0.04845755042902945 0.3782023333358317 chr17 81195210 4562298 0.05618925057278625 0.3947565970448395 chr18 78077248 5274466 0.06755445581278684 1.2960946878994042 chr19 59128983 3062227 0.051788934032570795 0.6421645345485177 chr20 63025520 3362886 0.05335752882324493 0.3728818566638207 chr21 48129895 2560352 0.05319670861530033 0.39213097058392005 chr22 51304566 1705326 0.033239263733368295 0.273864373546463 chrMT 16571 534929 32.28103313016716 19.25004516253002 chrX 155270560 9038559 0.05821167257978589 0.4076600135193045 chrY 59373566 657223 0.0110692862881101 0.5273378862252551