BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084339.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 = 3,298,543 number of mapped reads = 2,931,297 (88.87%) number of supplementary alignments = 20,978 (0.64%) number of secondary alignments = 0 number of mapped bases = 191,506,579 bp number of sequenced bases = 191,441,193 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 101,468 duplication rate = 2.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0715 >>>>>>> ACTG content number of A's = 53,225,643 bp (27.8%) number of C's = 36,800,600 bp (19.22%) number of T's = 57,969,408 bp (30.28%) number of G's = 43,203,500 bp (22.57%) number of N's = 242,042 bp (0.13%) GC percentage = 41.79% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 1,995,792 number of insertions = 14,858 mapped reads with insertion percentage = 0.5% number of deletions = 40,730 mapped reads with deletion percentage = 1.38% homopolymer indels = 45.26% >>>>>>> Coverage mean coverageData = 0.0619X std coverageData = 0.3983X There is a 5.17% of reference with a coverageData >= 1X There is a 0.74% of reference with a coverageData >= 2X There is a 0.14% 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 18405660 0.07384398853714391 0.6365198497388999 chr2 243199373 19188134 0.07889878071355061 0.5007628352428334 chr3 198022430 12793424 0.06460593378234981 0.29756520940044684 chr4 191154276 9568554 0.05005670916825319 0.27198131560751343 chr5 180915260 9548180 0.052777084697001236 0.26553700428611715 chr6 171115067 8992376 0.05255163182094304 0.29924523696871613 chr7 159138663 10666815 0.06702843167659389 0.5664870199345393 chr8 146364022 9613736 0.06568373749663699 0.3686328410362659 chr9 141213431 6852420 0.048525270942535205 0.33537662500329074 chr10 135534747 13962897 0.10302079215155063 0.573101453032302 chr11 135006516 10820133 0.08014526498854321 0.39875167306761766 chr12 133851895 7139317 0.053337436873792485 0.2669050804099291 chr13 115169878 4979589 0.04323690435792595 0.24018447804600404 chr14 107349540 5242949 0.04883997639859472 0.27012519355413933 chr15 102531392 4140195 0.04037977949231392 0.24947996875293624 chr16 90354753 3940972 0.04361665401265609 0.26903425433964523 chr17 81195210 5247849 0.06463249494643834 0.3177339626685871 chr18 78077248 5521254 0.07071527418589343 0.57123021949781 chr19 59128983 4319332 0.07304931999253225 0.46483495106060263 chr20 63025520 3909920 0.06203709227627158 0.2932449781951748 chr21 48129895 2047273 0.04253641110166561 0.2491843250162684 chr22 51304566 1713597 0.033400477454579774 0.20845841996355718 chrMT 16571 25389 1.5321344517530626 1.6794953328463444 chrX 155270560 12416410 0.07996628594628627 0.36151961229882595 chrY 59373566 450204 0.0075825662888430855 0.13778009305577874