BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008693.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 = 1,683,638 number of mapped reads = 1,299,376 (77.18%) number of supplementary alignments = 11,768 (0.7%) number of secondary alignments = 0 number of mapped bases = 81,854,145 bp number of sequenced bases = 81,813,168 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 120,341 duplication rate = 7.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9703 >>>>>>> ACTG content number of A's = 22,049,684 bp (26.95%) number of C's = 14,342,354 bp (17.53%) number of T's = 26,458,297 bp (32.34%) number of G's = 18,949,161 bp (23.16%) number of N's = 13,672 bp (0.02%) GC percentage = 40.69% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 622,702 number of insertions = 6,432 mapped reads with insertion percentage = 0.49% number of deletions = 25,886 mapped reads with deletion percentage = 1.97% homopolymer indels = 48.58% >>>>>>> Coverage mean coverageData = 0.0264X std coverageData = 0.2574X There is a 1.87% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 6733967 0.027016851444474434 0.33288866246923177 chr2 243199373 7617139 0.03132055361014438 0.28859322427994766 chr3 198022430 6048087 0.03054243400608709 0.24269533788369863 chr4 191154276 5156292 0.02697450513741058 0.23028314232000602 chr5 180915260 4651459 0.025710705664077203 0.21790056452535447 chr6 171115067 5349617 0.031263272684222486 0.2537078566031404 chr7 159138663 4302461 0.027035925267262048 0.29372463047846736 chr8 146364022 4325766 0.02955484511077456 0.3290305169064297 chr9 141213431 3009207 0.02130963732479526 0.22748609273825132 chr10 135534747 4012769 0.029606939097322402 0.27365740617125156 chr11 135006516 3573990 0.026472722249939403 0.24987798222585952 chr12 133851895 3880598 0.028991730001282388 0.23663247316112487 chr13 115169878 2718671 0.02360574698186274 0.20951326683650714 chr14 107349540 2452256 0.02284365633984086 0.2206091770067587 chr15 102531392 2143591 0.020906679975631268 0.19687280940841612 chr16 90354753 1886768 0.020881779179895494 0.20673412740273117 chr17 81195210 1939562 0.023887640662546474 0.21851437287734074 chr18 78077248 2024614 0.02593090883531141 0.3426624064387134 chr19 59128983 1257870 0.021273323777613425 0.24763033904481452 chr20 63025520 1611190 0.02556408895951989 0.21932869846393754 chr21 48129895 1000895 0.020795702961745502 0.20092867815965423 chr22 51304566 926316 0.018055235083754534 0.17901040390897488 chrMT 16571 109016 6.57872186349647 4.521060119352924 chrX 155270560 4919376 0.03168260615534587 0.2516326994980487 chrY 59373566 202668 0.0034134382293965634 0.08989518039070804