BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237287.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 = 2,658,791 number of mapped reads = 2,422,277 (91.1%) number of supplementary alignments = 28,052 (1.06%) number of secondary alignments = 0 number of mapped bases = 147,786,425 bp number of sequenced bases = 147,698,724 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,116,617 duplication rate = 24.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.5074 >>>>>>> ACTG content number of A's = 37,100,733 bp (25.12%) number of C's = 25,119,337 bp (17.01%) number of T's = 49,758,451 bp (33.69%) number of G's = 35,705,588 bp (24.17%) number of N's = 14,615 bp (0.01%) GC percentage = 41.18% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 950,715 number of insertions = 9,893 mapped reads with insertion percentage = 0.4% number of deletions = 51,992 mapped reads with deletion percentage = 2.12% homopolymer indels = 42.2% >>>>>>> Coverage mean coverageData = 0.0477X std coverageData = 0.7882X There is a 1.08% of reference with a coverageData >= 1X There is a 0.7% of reference with a coverageData >= 2X There is a 0.56% of reference with a coverageData >= 3X There is a 0.46% of reference with a coverageData >= 4X There is a 0.38% of reference with a coverageData >= 5X There is a 0.31% of reference with a coverageData >= 6X There is a 0.25% of reference with a coverageData >= 7X There is a 0.2% of reference with a coverageData >= 8X There is a 0.16% of reference with a coverageData >= 9X There is a 0.13% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% 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 7675244 0.03079327934753671 0.5410437200217034 chr2 243199373 12745126 0.05240608083311136 1.2370942184472702 chr3 198022430 12096762 0.06108783737276631 0.7379096958168512 chr4 191154276 7218406 0.037762199993893936 0.5807705779270682 chr5 180915260 6763302 0.03738381162539854 0.5741607236985413 chr6 171115067 9648310 0.05638492371919534 0.7941125127032157 chr7 159138663 12787957 0.08035732334888349 1.0947855491464233 chr8 146364022 10212950 0.06977773540549466 1.2545650007124176 chr9 141213431 5486228 0.03885061046353303 0.5897654328436912 chr10 135534747 5784021 0.04267555832011108 0.6399438583279979 chr11 135006516 3310660 0.02452222380140526 0.4879773216934688 chr12 133851895 4357564 0.03255511623499988 0.5335697384354634 chr13 115169878 9624064 0.08356407219603028 0.8997906141805759 chr14 107349540 10376335 0.09665933361242163 0.9456031379868562 chr15 102531392 7968236 0.07771508651711273 0.8415234169319674 chr16 90354753 2332728 0.025817435414825382 0.48616521917289496 chr17 81195210 3806528 0.0468811891735978 0.7119455299820545 chr18 78077248 2240078 0.028690534789340937 1.0395493575263077 chr19 59128983 715664 0.01210343834258066 0.45897933937194807 chr20 63025520 4014934 0.06370330621627557 0.7764732549635244 chr21 48129895 2134687 0.044352621172350365 0.6404760153296504 chr22 51304566 608510 0.01186073769730359 0.3074088658087846 chrMT 16571 12733 0.7683905618248748 2.853945119022138 chrX 155270560 5466978 0.03520936615415054 0.5860264609909496 chrY 59373566 398420 0.006710393645549267 0.2525007705474857