BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081907.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 = 3,258,131 number of mapped reads = 2,974,135 (91.28%) number of supplementary alignments = 24,695 (0.76%) number of secondary alignments = 0 number of mapped bases = 199,079,908 bp number of sequenced bases = 199,012,460 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 128,633 duplication rate = 3.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7653 >>>>>>> ACTG content number of A's = 55,710,656 bp (27.99%) number of C's = 38,527,755 bp (19.36%) number of T's = 60,826,912 bp (30.56%) number of G's = 43,944,922 bp (22.08%) number of N's = 2,215 bp (0%) GC percentage = 41.44% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,617,528 number of insertions = 13,652 mapped reads with insertion percentage = 0.45% number of deletions = 37,812 mapped reads with deletion percentage = 1.26% homopolymer indels = 46.86% >>>>>>> Coverage mean coverageData = 0.0643X std coverageData = 0.4438X There is a 5.26% of reference with a coverageData >= 1X There is a 0.85% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.04% 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 15475935 0.06208985533480376 0.6934663122891807 chr2 243199373 16940169 0.0696554797450074 0.5346616201650675 chr3 198022430 13250081 0.06691202102711294 0.30350014310291684 chr4 191154276 13350742 0.06984275884050849 0.33067166884428045 chr5 180915260 12400387 0.06854251542959947 0.3103250821804119 chr6 171115067 11957859 0.06988197596883738 0.35851048090000176 chr7 159138663 11204775 0.07040887983330613 0.6092029482004563 chr8 146364022 10007008 0.06837068196991744 0.5494255238125243 chr9 141213431 8639463 0.06118017910066926 0.4273212472427176 chr10 135534747 9141221 0.06744559017031994 0.4790193994734191 chr11 135006516 8960440 0.06637042615039411 0.3891997016842784 chr12 133851895 9160107 0.06843464562081844 0.31110998871003587 chr13 115169878 6521172 0.05662220116270333 0.2801244880907056 chr14 107349540 6056928 0.05642248676612867 0.293938438475043 chr15 102531392 5660253 0.05520507319358348 0.28225707950272594 chr16 90354753 5794022 0.06412525968611746 0.3362775079674147 chr17 81195210 5015415 0.06176983839317615 0.31039633822355245 chr18 78077248 5292205 0.06778165388206306 0.7841684865528142 chr19 59128983 3693510 0.062465305719870065 0.5913698094489671 chr20 63025520 3923362 0.06225037096084253 0.3016760181572778 chr21 48129895 2486794 0.051668386145450766 0.28849739778405326 chr22 51304566 2081422 0.04056991730521607 0.2360946406152436 chrMT 16571 14634 0.8831090459236015 1.1631338990842641 chrX 155270560 11557628 0.07443541132330558 0.3616681610971762 chrY 59373566 494376 0.008326533730515697 0.17794028222740205