BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084274.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 = 3,116,350 number of mapped reads = 2,103,287 (67.49%) number of supplementary alignments = 13,148 (0.42%) number of secondary alignments = 0 number of mapped bases = 132,418,968 bp number of sequenced bases = 132,376,209 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 80,829 duplication rate = 3.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7411 >>>>>>> ACTG content number of A's = 37,147,853 bp (28.06%) number of C's = 25,329,651 bp (19.13%) number of T's = 40,330,331 bp (30.47%) number of G's = 29,566,918 bp (22.34%) number of N's = 1,456 bp (0%) GC percentage = 41.47% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,080,055 number of insertions = 9,434 mapped reads with insertion percentage = 0.45% number of deletions = 26,740 mapped reads with deletion percentage = 1.26% homopolymer indels = 46.46% >>>>>>> Coverage mean coverageData = 0.0428X std coverageData = 0.2991X There is a 3.69% of reference with a coverageData >= 1X There is a 0.45% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% 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 9824718 0.039417025163600294 0.40717352474348256 chr2 243199373 11916521 0.04899897912154568 0.3986748992123089 chr3 198022430 9892475 0.04995633575449004 0.2525016918713287 chr4 191154276 8930132 0.046716883278091044 0.24952312888547715 chr5 180915260 7837025 0.043318761501931896 0.2355225328417406 chr6 171115067 7737961 0.04522080454785434 0.2674285234088702 chr7 159138663 7437114 0.0467335458260071 0.3458822615851329 chr8 146364022 6424472 0.04389379242393325 0.2995871168528424 chr9 141213431 5498725 0.0389391077113621 0.2890512511100499 chr10 135534747 6230720 0.04597138474018032 0.2929695069371102 chr11 135006516 6356538 0.04708319411783058 0.2887292556162574 chr12 133851895 5419318 0.040487420816866286 0.2298997542848985 chr13 115169878 4095531 0.035560782655339795 0.21415755597775255 chr14 107349540 3907531 0.03640007213817591 0.2269689155485673 chr15 102531392 3536391 0.03449081233579663 0.21719083694221095 chr16 90354753 3561170 0.03941320054297531 0.24100834367082485 chr17 81195210 3502068 0.04313146058739179 0.26064565241834353 chr18 78077248 3625128 0.04643001761537497 0.5266437311689014 chr19 59128983 2632853 0.04452728368421287 0.34302214239419565 chr20 63025520 2694209 0.042747905927630586 0.2375956003001729 chr21 48129895 1975308 0.04104118656398482 0.23521628484898377 chr22 51304566 1575420 0.030707208399345976 0.19776469942119348 chrMT 16571 58923 3.5557902359543783 2.676962975095058 chrX 155270560 7436707 0.0478951515341994 0.2756844266891662 chrY 59373566 312010 0.0052550321804824725 0.10541728958736743