BamQC report ----------------------------------- >>>>>>> Input bam file = SRR536746.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP014781/SRP014781.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 = 19,227,472 number of mapped reads = 15,622,250 (81.25%) number of supplementary alignments = 343 (0%) number of secondary alignments = 0 number of mapped bases = 778,863,659 bp number of sequenced bases = 778,795,817 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 111,139 duplication rate = 0.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5215 >>>>>>> ACTG content number of A's = 245,163,471 bp (31.48%) number of C's = 143,798,281 bp (18.46%) number of T's = 243,635,655 bp (31.28%) number of G's = 146,181,709 bp (18.77%) number of N's = 16,701 bp (0%) GC percentage = 37.23% >>>>>>> Mismatches and indels general error rate = 0.0036 number of mismatches = 2,712,767 number of insertions = 52,932 mapped reads with insertion percentage = 0.34% number of deletions = 40,645 mapped reads with deletion percentage = 0.26% homopolymer indels = 49.28% >>>>>>> Coverage mean coverageData = 0.2516X std coverageData = 0.6736X There is a 20.19% of reference with a coverageData >= 1X There is a 4.04% of reference with a coverageData >= 2X There is a 0.75% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.02% 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 58838742 0.23606256932856348 0.5482883949023869 chr2 243199373 73211617 0.3010353854818532 1.466992620916798 chr3 198022430 64848530 0.3274807303394873 0.6273388390842697 chr4 191154276 67977139 0.35561401200358184 0.6564259256875218 chr5 180915260 56851600 0.3142443594863142 0.6106640561568447 chr6 171115067 52908297 0.3091971848393689 0.6082723985757661 chr7 159138663 45008220 0.28282391690069686 0.5924650204882278 chr8 146364022 43592872 0.29783871339638374 0.5969681421651536 chr9 141213431 32758294 0.23197718353008503 0.5420007125379208 chr10 135534747 32298723 0.23830584934799046 0.5304411073701594 chr11 135006516 35304140 0.2614995264376721 0.5661999141782933 chr12 133851895 35775316 0.26727537925406286 0.5732332311391396 chr13 115169878 35386156 0.3072518319416818 0.6179535876569446 chr14 107349540 24325121 0.2265973473197929 0.532413206816683 chr15 102531392 19262532 0.18786960387702528 0.4813303018431068 chr16 90354753 12845801 0.1421707278641999 0.4161743428699651 chr17 81195210 9647486 0.11881841305663228 0.3791296234131031 chr18 78077248 25213703 0.3229327831841614 0.6574534633601067 chr19 59128983 3622765 0.06126885355021242 0.2644637547783338 chr20 63025520 12145401 0.19270608159996142 0.4913137713520107 chr21 48129895 10320700 0.21443429286517246 0.5313035022079572 chr22 51304566 2998333 0.058441835371923816 0.2599850166819202 chrMT 16571 3136 0.1892462736105244 0.4753614206411652 chrX 155270560 20568658 0.13246978693192063 0.3812678269567 chrY 59373566 3150377 0.05306026254175132 0.25107372122657007