BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081883.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,421,657 number of mapped reads = 2,221,574 (91.74%) number of supplementary alignments = 15,515 (0.64%) number of secondary alignments = 0 number of mapped bases = 150,291,810 bp number of sequenced bases = 150,238,226 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 85,903 duplication rate = 2.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2518 >>>>>>> ACTG content number of A's = 41,542,687 bp (27.65%) number of C's = 28,825,369 bp (19.19%) number of T's = 46,107,210 bp (30.69%) number of G's = 33,761,215 bp (22.47%) number of N's = 1,745 bp (0%) GC percentage = 41.66% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,197,927 number of insertions = 10,657 mapped reads with insertion percentage = 0.48% number of deletions = 30,027 mapped reads with deletion percentage = 1.34% homopolymer indels = 46.4% >>>>>>> Coverage mean coverageData = 0.0485X std coverageData = 0.4082X There is a 4.17% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 12277769 0.04925872983080752 0.7607984518668119 chr2 243199373 12312594 0.05062757295842206 0.46851146297236224 chr3 198022430 10288183 0.05195463463406645 0.2625498187181148 chr4 191154276 10363408 0.05421488975742295 0.2862779710048197 chr5 180915260 9445625 0.05221021709279803 0.25685639126779647 chr6 171115067 8912091 0.05208244461605476 0.2936001285974796 chr7 159138663 8251063 0.0518482614121246 0.47169073525263616 chr8 146364022 7458946 0.050961608584382846 0.5194746454867211 chr9 141213431 6518197 0.046158477659253246 0.366939658879078 chr10 135534747 7025955 0.05183877312288044 0.5062477537257335 chr11 135006516 6696985 0.04960490203302483 0.3275875160272593 chr12 133851895 6410729 0.04789419679116235 0.25063099321903093 chr13 115169878 4940125 0.04289424531647068 0.231817472341362 chr14 107349540 4534768 0.04224301287178315 0.24519326058016064 chr15 102531392 4175332 0.04072247453735925 0.23050038279458931 chr16 90354753 4217350 0.04667546376890654 0.2927997345867319 chr17 81195210 3766377 0.046386689559642744 0.2613688770947357 chr18 78077248 3876369 0.04964786924867024 0.6607763199689689 chr19 59128983 2978135 0.05036675499729126 0.5785898872063063 chr20 63025520 3016361 0.04785935919291106 0.2549970762580971 chr21 48129895 1942849 0.04036678243324653 0.24911831736636988 chr22 51304566 1673846 0.03262567312234938 0.20238659374587414 chrMT 16571 6843 0.41295033492245486 0.7787372919325599 chrX 155270560 8791418 0.056619992869221314 0.30189338612410516 chrY 59373566 410492 0.006913716450852893 0.1709815316789478