BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004108.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 = 4,287,254 number of mapped reads = 3,792,607 (88.46%) number of supplementary alignments = 24,531 (0.57%) number of secondary alignments = 0 number of mapped bases = 261,116,596 bp number of sequenced bases = 260,997,463 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 214,982 duplication rate = 4.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1132 >>>>>>> ACTG content number of A's = 73,756,148 bp (28.26%) number of C's = 48,952,822 bp (18.76%) number of T's = 83,014,636 bp (31.81%) number of G's = 55,238,235 bp (21.16%) number of N's = 35,622 bp (0.01%) GC percentage = 39.92% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 2,453,051 number of insertions = 22,698 mapped reads with insertion percentage = 0.59% number of deletions = 70,502 mapped reads with deletion percentage = 1.84% homopolymer indels = 46.71% >>>>>>> Coverage mean coverageData = 0.0843X std coverageData = 0.7507X There is a 6.34% of reference with a coverageData >= 1X There is a 1.41% of reference with a coverageData >= 2X There is a 0.35% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 21905442 0.08788520530907724 1.5504987881900505 chr2 243199373 21877011 0.0899550468824605 0.7671460748486517 chr3 198022430 17085074 0.08627847865517053 0.3801884191402744 chr4 191154276 13605869 0.07117742424971964 0.4071080504942162 chr5 180915260 18771189 0.10375680304690715 0.4123420821096771 chr6 171115067 10559429 0.06170952204927693 0.35702269795275665 chr7 159138663 15467088 0.09719252197060371 0.9995776938610694 chr8 146364022 14355106 0.09807810556066845 1.0046471071613052 chr9 141213431 11446777 0.08106011530872018 0.7126900960934561 chr10 135534747 14328016 0.10571470650253252 0.7739252566769977 chr11 135006516 13643880 0.10106089990500904 0.6563908220797399 chr12 133851895 8767811 0.06550382420809209 0.3456965136439219 chr13 115169878 9684482 0.08408867117146725 0.3629128619618317 chr14 107349540 7244805 0.06748799296205647 0.39630051266310606 chr15 102531392 7851350 0.07657508443852981 0.34881887501464603 chr16 90354753 7096586 0.07854136904120583 0.4782844748181938 chr17 81195210 6922849 0.08526179068937688 0.42623423819640577 chr18 78077248 7917691 0.10140842822738834 1.4318265772827075 chr19 59128983 4983014 0.08427362939761707 0.9693704102982598 chr20 63025520 5552783 0.08810372369795601 0.3917226102939407 chr21 48129895 4144044 0.08610124746791989 0.4498025702154573 chr22 51304566 2948352 0.057467633582554814 0.30039332877596575 chrMT 16571 31112 1.877496831814616 1.780904153456198 chrX 155270560 14255109 0.09180818952414417 0.44215158687338324 chrY 59373566 671727 0.011313570082686292 0.27522467654334637