BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081699.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 = 2,863,723 number of mapped reads = 2,658,702 (92.84%) number of supplementary alignments = 23,660 (0.83%) number of secondary alignments = 0 number of mapped bases = 181,555,308 bp number of sequenced bases = 181,487,344 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 112,102 duplication rate = 3.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.115 >>>>>>> ACTG content number of A's = 51,743,978 bp (28.51%) number of C's = 33,804,899 bp (18.63%) number of T's = 57,281,299 bp (31.56%) number of G's = 38,655,095 bp (21.3%) number of N's = 2,073 bp (0%) GC percentage = 39.93% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,533,174 number of insertions = 14,654 mapped reads with insertion percentage = 0.55% number of deletions = 41,102 mapped reads with deletion percentage = 1.53% homopolymer indels = 47.81% >>>>>>> Coverage mean coverageData = 0.0586X std coverageData = 0.467X There is a 4.83% of reference with a coverageData >= 1X There is a 0.74% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.03% 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 0.01% 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 14341809 0.057539712207978815 0.7595771334210886 chr2 243199373 15647578 0.0643405359437337 0.5548337101132218 chr3 198022430 12320186 0.06221611359884837 0.2921597257294896 chr4 191154276 12431388 0.06503327186884378 0.3314214769631791 chr5 180915260 11413916 0.06308984659447743 0.29491503821983533 chr6 171115067 10508016 0.06140906341111388 0.34099214808539785 chr7 159138663 10088770 0.06339609627108655 0.6364524724395093 chr8 146364022 9333321 0.06376786366256046 0.7568221511252756 chr9 141213431 7624485 0.05399263332111802 0.4384573011875873 chr10 135534747 8555089 0.06312100173101735 0.4820954705795273 chr11 135006516 8300178 0.06147983257341446 0.3834225279527471 chr12 133851895 8118650 0.06065397878752482 0.29168637038625034 chr13 115169878 6005102 0.05214125519869006 0.2663410582288028 chr14 107349540 5483278 0.05107872842305612 0.28561322002306866 chr15 102531392 5052439 0.049276996063800635 0.26168083023890876 chr16 90354753 4914407 0.05439013263640929 0.3172291259221138 chr17 81195210 4352765 0.053608642677320496 0.30205713187794336 chr18 78077248 4948666 0.0633816652963998 0.7959136165564598 chr19 59128983 3258803 0.05511346271590702 0.5960170731268026 chr20 63025520 3610756 0.05729038015077067 0.2932839197974924 chr21 48129895 2358911 0.049011347313348594 0.28954623888155784 chr22 51304566 1782167 0.03473700566924199 0.21372209118021368 chrMT 16571 16388 0.9889566109468348 1.1708468333666904 chrX 155270560 10593235 0.06822436268665483 0.35113161729205894 chrY 59373566 495005 0.008337127670586603 0.21305530826998803