BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708581.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 6,451,402 number of mapped reads = 6,320,976 (97.98%) number of supplementary alignments = 165 (0%) number of secondary alignments = 0 number of mapped bases = 315,281,821 bp number of sequenced bases = 315,254,714 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,866 duplication rate = 1.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7557 >>>>>>> ACTG content number of A's = 97,704,940 bp (30.99%) number of C's = 59,775,518 bp (18.96%) number of T's = 97,027,980 bp (30.78%) number of G's = 60,735,580 bp (19.27%) number of N's = 10,696 bp (0%) GC percentage = 38.23% >>>>>>> Mismatches and indels general error rate = 0.0016 number of mismatches = 465,985 number of insertions = 19,923 mapped reads with insertion percentage = 0.31% number of deletions = 16,107 mapped reads with deletion percentage = 0.25% homopolymer indels = 49.21% >>>>>>> Coverage mean coverageData = 0.1018X std coverageData = 0.336X There is a 9.23% of reference with a coverageData >= 1X There is a 0.86% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 24451195 0.09809883282096216 0.3328334853472429 chr2 243199373 28395137 0.11675662091447908 0.3605465753723244 chr3 198022430 24074266 0.1215734298382259 0.3643700195408314 chr4 191154276 24278677 0.12701090191673242 0.37197150996772493 chr5 180915260 21685108 0.119863343755524 0.3617601414055744 chr6 171115067 20881724 0.12203322808505226 0.3650283517931752 chr7 159138663 17477997 0.10982872842157786 0.34809543257717257 chr8 146364022 16686581 0.11400739588858798 0.35258970515532617 chr9 141213431 13112588 0.09285652155849113 0.32179048995459547 chr10 135534747 13772132 0.1016132933055167 0.33363250003215766 chr11 135006516 14892820 0.11031186079937061 0.35085477272071897 chr12 133851895 15826705 0.11824042535968579 0.3618431415956683 chr13 115169878 11506259 0.09990684369744665 0.3321264748304875 chr14 107349540 9473573 0.08824977731623256 0.3134159239329982 chr15 102531392 8602663 0.08390272317769762 0.30624840611415444 chr16 90354753 5863761 0.06489709512016485 0.26774787658017374 chr17 81195210 5214183 0.06421786457600147 0.2654870046108069 chr18 78077248 9005777 0.11534444707887245 0.35453942985692527 chr19 59128983 2648691 0.044795138790058336 0.2198914113373591 chr20 63025520 5233845 0.08304326564858172 0.303455886703343 chr21 48129895 3773302 0.07839830109747799 0.2973040021264998 chr22 51304566 1839961 0.0358634940991412 0.19789050536829575 chrMT 16571 337 0.020336732846539134 0.15655502435912413 chrX 155270560 16211197 0.10440612180441676 0.337710414899631 chrY 59373566 373342 0.006288017128700001 0.08435528154825306