BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084971.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 = 2,493,471 number of mapped reads = 2,298,896 (92.2%) number of supplementary alignments = 20,407 (0.82%) number of secondary alignments = 0 number of mapped bases = 159,144,402 bp number of sequenced bases = 159,080,205 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 80,833 duplication rate = 2.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0564 >>>>>>> ACTG content number of A's = 46,484,532 bp (29.22%) number of C's = 29,526,423 bp (18.56%) number of T's = 49,802,287 bp (31.31%) number of G's = 33,244,343 bp (20.9%) number of N's = 22,620 bp (0.01%) GC percentage = 39.46% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,325,670 number of insertions = 13,258 mapped reads with insertion percentage = 0.57% number of deletions = 38,979 mapped reads with deletion percentage = 1.68% homopolymer indels = 47.98% >>>>>>> Coverage mean coverageData = 0.0514X std coverageData = 0.469X There is a 4.53% of reference with a coverageData >= 1X There is a 0.44% of reference with a coverageData >= 2X There is a 0.05% 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 11862725 0.04759356246498579 0.8768936391606295 chr2 243199373 14104219 0.05799447106304834 0.47720250261909325 chr3 198022430 11145054 0.05628177575641305 0.27228286946340186 chr4 191154276 11279507 0.0590073485983646 0.27479666933624636 chr5 180915260 10055357 0.05558048005458467 0.2595191756270106 chr6 171115067 9448099 0.05521488648337437 0.34848056491850565 chr7 159138663 8723116 0.05481456131122579 0.36842623569852667 chr8 146364022 8283030 0.056591981327214415 0.8962917477120221 chr9 141213431 6476894 0.045865991316364235 0.4188975739314128 chr10 135534747 7254682 0.053526362505402394 0.5939948722988314 chr11 135006516 7204139 0.05336141701486467 0.3912143172391015 chr12 133851895 7080062 0.05289474609231345 0.2578567859894216 chr13 115169878 5631476 0.0488971256876733 0.2403055522200497 chr14 107349540 4870389 0.045369444526730154 0.25428224816086614 chr15 102531392 4482267 0.04371604552096591 0.2280023068888945 chr16 90354753 4382377 0.048501897847034126 0.29932863528104353 chr17 81195210 3916602 0.04823686027784151 0.28116472183598895 chr18 78077248 4492714 0.05754191028864132 0.8256059656007694 chr19 59128983 2754094 0.04657773329197967 0.5886340740559102 chr20 63025520 3095814 0.04912000726055096 0.25321101847371613 chr21 48129895 1956533 0.04065109637160023 0.24025227655538295 chr22 51304566 1544453 0.0301036168983478 0.18778719267966512 chrMT 16571 12083 0.7291654094502444 0.9244757343258029 chrX 155270560 8734465 0.05625319442397838 0.2950774084511537 chrY 59373566 354251 0.005966476731412764 0.13092875533289658