BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549002.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 9,488,986 number of mapped reads = 8,199,908 (86.42%) number of secondary alignments = 0 number of mapped bases = 325,570,489 bp number of sequenced bases = 325,535,683 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 713,385 duplication rate = 7.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5194 >>>>>>> ACTG content number of A's = 97,629,192 bp (29.99%) number of C's = 64,506,624 bp (19.82%) number of T's = 98,180,945 bp (30.16%) number of G's = 65,215,690 bp (20.03%) number of N's = 3,232 bp (0%) GC percentage = 39.85% >>>>>>> Mismatches and indels general error rate = 0.0029 number of mismatches = 919,794 number of insertions = 9,718 mapped reads with insertion percentage = 0.12% number of deletions = 26,849 mapped reads with deletion percentage = 0.33% homopolymer indels = 43.47% >>>>>>> Coverage mean coverageData = 0.1052X std coverageData = 0.8506X There is a 7.8% of reference with a coverageData >= 1X There is a 1.89% of reference with a coverageData >= 2X There is a 0.48% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.05% 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% 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 25960993 0.10415618182150888 1.299622103260258 chr2 243199373 28637856 0.11775464569145908 0.579208351392216 chr3 198022430 22905068 0.11566905829809279 0.43268460132416553 chr4 191154276 23214199 0.12144221665227097 0.4755679341484488 chr5 180915260 21079441 0.11651554987677656 0.4402725941574803 chr6 171115067 19967040 0.11668779582104245 0.5095383034443279 chr7 159138663 18206319 0.11440537866024424 0.8538454725360449 chr8 146364022 17503074 0.1195859047929142 2.60821303980563 chr9 141213431 13672412 0.09682090367169112 0.5243115797326556 chr10 135534747 15357908 0.11331343688567183 0.6366410637914919 chr11 135006516 15173560 0.11239131598655579 0.5505020374407369 chr12 133851895 15013348 0.11216388083261727 0.4404435426946104 chr13 115169878 11372840 0.09874838974822914 0.3963365459621709 chr14 107349540 10259164 0.09556784314120023 0.45732915534027796 chr15 102531392 9239874 0.09011751249802596 0.3777949187977858 chr16 90354753 8448321 0.09350167777006706 0.42406402835221146 chr17 81195210 7654299 0.09427032703037531 0.42966835527817115 chr18 78077248 8995659 0.11521485747038625 1.0953109133246177 chr19 59128983 5223527 0.08834122853085431 0.9787882871032657 chr20 63025520 6500215 0.10313623751140807 0.43357895167808763 chr21 48129895 4286685 0.08906491485177767 0.4522330929009196 chr22 51304566 3144266 0.06128628005546329 0.34208862729583517 chrMT 16571 26191 1.5805322551445296 2.0379089113034805 chrX 155270560 10953952 0.07054751396530032 0.4166793860980834 chrY 59373566 2774278 0.04672581060736692 0.4672659452728128