BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472827.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 4,000,000 number of mapped reads = 3,439,317 (85.98%) number of supplementary alignments = 24,239 (0.61%) number of secondary alignments = 0 number of mapped bases = 224,695,802 bp number of sequenced bases = 224,603,829 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 112,208 duplication rate = 2.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.796 >>>>>>> ACTG content number of A's = 60,800,145 bp (27.07%) number of C's = 44,147,814 bp (19.66%) number of T's = 67,497,249 bp (30.05%) number of G's = 52,154,541 bp (23.22%) number of N's = 4,080 bp (0%) GC percentage = 42.88% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,844,543 number of insertions = 17,500 mapped reads with insertion percentage = 0.5% number of deletions = 51,797 mapped reads with deletion percentage = 1.49% homopolymer indels = 45.3% >>>>>>> Coverage mean coverageData = 0.0726X std coverageData = 0.4829X There is a 6.16% of reference with a coverageData >= 1X There is a 0.79% 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 0.01% 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 16589743 0.06655848211507566 0.6074104187588018 chr2 243199373 22317179 0.09176495286441384 0.7371351820465267 chr3 198022430 16277100 0.08219826410573793 0.3229959521498344 chr4 191154276 12403205 0.06488583598307787 0.3317724714619696 chr5 180915260 11291668 0.062414126923289945 0.2855551747381984 chr6 171115067 14004751 0.08184405526370159 0.3690917649400972 chr7 159138663 13835251 0.08693833879954113 0.6554858367655952 chr8 146364022 12700290 0.08677193907666735 0.4914116175778073 chr9 141213431 13041124 0.09235045071598041 0.5865387911893817 chr10 135534747 9424600 0.06953641194313072 0.42432878868978013 chr11 135006516 7518724 0.055691563805705495 0.46328091653097314 chr12 133851895 9456778 0.0706510580220026 0.31578671482484094 chr13 115169878 9019417 0.07831402756196373 0.33211665640904403 chr14 107349540 4584066 0.04270224166773327 0.30959788012106415 chr15 102531392 4298023 0.04191909342262709 0.261919065137758 chr16 90354753 7512396 0.08314334056117667 0.38022368399341394 chr17 81195210 4956563 0.06104501731075023 0.31571901135829833 chr18 78077248 3870014 0.049566475498726593 1.016749270454613 chr19 59128983 5158608 0.08724330672151083 0.4916416303184844 chr20 63025520 9775154 0.15509834746305942 0.48229749784701015 chr21 48129895 3063338 0.06364730278343636 0.355612063744091 chr22 51304566 2579109 0.05027055486640312 0.2719431027054047 chrMT 16571 243471 14.692595498159434 10.347392783996863 chrX 155270560 9659145 0.06220847661011849 0.3428355021120272 chrY 59373566 1116085 0.018797675046164482 0.2398004987046519