BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548957.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 = 8,112,095 number of mapped reads = 6,780,913 (83.59%) number of secondary alignments = 0 number of mapped bases = 267,721,953 bp number of sequenced bases = 267,697,448 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 332,158 duplication rate = 2.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 35.6166 >>>>>>> ACTG content number of A's = 75,128,207 bp (28.06%) number of C's = 58,089,747 bp (21.7%) number of T's = 76,420,028 bp (28.55%) number of G's = 58,059,104 bp (21.69%) number of N's = 362 bp (0%) GC percentage = 43.39% >>>>>>> Mismatches and indels general error rate = 0.0034 number of mismatches = 888,591 number of insertions = 9,610 mapped reads with insertion percentage = 0.14% number of deletions = 19,290 mapped reads with deletion percentage = 0.28% homopolymer indels = 37.88% >>>>>>> Coverage mean coverageData = 0.0865X std coverageData = 0.8785X There is a 7.06% of reference with a coverageData >= 1X There is a 1.05% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 21384553 0.08579538503938171 1.540718468065362 chr2 243199373 22458980 0.09234801768999626 0.9498995298338017 chr3 198022430 17649906 0.08913084240002508 0.35583474838925194 chr4 191154276 18102599 0.09470151219635808 0.4510900723232025 chr5 180915260 16365180 0.09045770931650542 0.38508402623263943 chr6 171115067 15378071 0.08986976582255027 0.39312878632025444 chr7 159138663 15587585 0.09794970440338562 1.2696683709770469 chr8 146364022 13462276 0.09197804088767116 1.51833834881047 chr9 141213431 11510950 0.08151455508506128 0.9560862598252119 chr10 135534747 13177297 0.0972244925502388 0.7618063317063664 chr11 135006516 12039889 0.08918005853880416 0.6200882506102546 chr12 133851895 12814534 0.09573666476668112 0.4124538242140768 chr13 115169878 8194632 0.07115256299915504 0.3073113425398598 chr14 107349540 8071522 0.0751891624314366 0.5693493178291358 chr15 102531392 7722079 0.07531429008590852 0.3345032019524067 chr16 90354753 7681864 0.08501892534640651 0.48671631305419316 chr17 81195210 8030696 0.09890603152575134 0.43506030239859 chr18 78077248 7018070 0.08988623676900087 1.8008770774471397 chr19 59128983 6073756 0.10272045436668512 1.5815492259392632 chr20 63025520 5353968 0.08494920787642847 0.4083548337361184 chr21 48129895 3362816 0.06986958936852034 0.5224169520180063 chr22 51304566 3055206 0.05955037218324778 0.4302425183240747 chrMT 16571 8942 0.5396174038983766 0.8677855389123406 chrX 155270560 10523360 0.06777434176833007 0.520037342864794 chrY 59373566 2693222 0.045360623951743104 0.48261925724324345