BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472825.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 = 2,709,141 number of mapped reads = 2,263,084 (83.54%) number of supplementary alignments = 14,974 (0.55%) number of secondary alignments = 0 number of mapped bases = 147,135,848 bp number of sequenced bases = 147,077,791 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 67,137 duplication rate = 2.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8899 >>>>>>> ACTG content number of A's = 40,139,929 bp (27.29%) number of C's = 29,440,486 bp (20.02%) number of T's = 43,482,485 bp (29.56%) number of G's = 34,011,737 bp (23.12%) number of N's = 3,154 bp (0%) GC percentage = 43.14% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,223,120 number of insertions = 11,226 mapped reads with insertion percentage = 0.49% number of deletions = 32,327 mapped reads with deletion percentage = 1.41% homopolymer indels = 45.55% >>>>>>> Coverage mean coverageData = 0.0475X std coverageData = 0.3264X There is a 4.12% of reference with a coverageData >= 1X There is a 0.48% 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% 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 12385484 0.04969088522351164 0.4314425522236567 chr2 243199373 13296895 0.05467487368892189 0.4488134971316233 chr3 198022430 9863638 0.04981071083715113 0.24852201134025925 chr4 191154276 8983228 0.0469946484482513 0.25792626011788833 chr5 180915260 8569034 0.047364904430947395 0.24361297239894084 chr6 171115067 8292656 0.04846245363069051 0.2723268211991934 chr7 159138663 8159396 0.0512722417430389 0.3498472605463314 chr8 146364022 7402274 0.05057440960456799 0.34474907284483486 chr9 141213431 6346439 0.0449421769236667 0.343398010889284 chr10 135534747 7138188 0.05266684859787284 0.3051073024805235 chr11 135006516 6820711 0.05052134668818504 0.3696354145697136 chr12 133851895 6995556 0.0522634065061238 0.25981739815778837 chr13 115169878 4296143 0.03730266172549041 0.22509299495129378 chr14 107349540 4709870 0.04387415167312315 0.2551997537558186 chr15 102531392 4498188 0.04387132479387386 0.24377294746759515 chr16 90354753 4530833 0.050144932608027826 0.2809074715601835 chr17 81195210 4361540 0.05371671555501858 0.28051380703183776 chr18 78077248 3786767 0.04850026220186449 0.6343096107366697 chr19 59128983 3310116 0.05598127740502488 0.35460886906049754 chr20 63025520 3569944 0.056642832934976184 0.278880588738051 chr21 48129895 2190085 0.04550363137089744 0.2740906935235253 chr22 51304566 1914520 0.037316756563148784 0.2293437140331142 chrMT 16571 21780 1.314344336491461 1.3843834012009533 chrX 155270560 4820688 0.031047018829583665 0.22864705453213977 chrY 59373566 871875 0.014684565181751085 0.16721163976307546