BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081037.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 = 2,762,117 number of mapped reads = 1,881,932 (68.13%) number of supplementary alignments = 9,203 (0.33%) number of secondary alignments = 0 number of mapped bases = 119,219,956 bp number of sequenced bases = 119,178,037 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 59,557 duplication rate = 2.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7842 >>>>>>> ACTG content number of A's = 33,489,963 bp (28.1%) number of C's = 22,924,679 bp (19.24%) number of T's = 35,931,513 bp (30.15%) number of G's = 26,830,386 bp (22.51%) number of N's = 1,496 bp (0%) GC percentage = 41.75% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 926,232 number of insertions = 7,894 mapped reads with insertion percentage = 0.42% number of deletions = 24,017 mapped reads with deletion percentage = 1.26% homopolymer indels = 46.9% >>>>>>> Coverage mean coverageData = 0.0385X std coverageData = 0.3031X There is a 3.37% of reference with a coverageData >= 1X There is a 0.36% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% 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 8891369 0.03567240460355764 0.46242122809433217 chr2 243199373 9597918 0.039465225101546625 0.31199922517009754 chr3 198022430 8239676 0.04160981157538568 0.22580876774742803 chr4 191154276 8594999 0.04496367635532254 0.25093512500402537 chr5 180915260 6921807 0.03825994004043661 0.2171653959935651 chr6 171115067 7535125 0.044035426757598146 0.3090016913926271 chr7 159138663 6350310 0.03990425632770334 0.46119746860851146 chr8 146364022 5515200 0.037681391400955076 0.30455936101061876 chr9 141213431 5165030 0.03657605344919351 0.2853746768252321 chr10 135534747 5212697 0.038460225996511437 0.28085586360798487 chr11 135006516 5245875 0.03885645786163388 0.28009875761174013 chr12 133851895 5500038 0.041090475409406794 0.22658774629264058 chr13 115169878 3985427 0.034604768792062104 0.2055416872039284 chr14 107349540 3742332 0.03486118338280723 0.22095306844319929 chr15 102531392 3499073 0.03412684575666348 0.2123318508687383 chr16 90354753 2858115 0.031632148892045554 0.22019977100364746 chr17 81195210 3309252 0.0407567392214393 0.25090979075792597 chr18 78077248 3537898 0.04531279073770633 0.5401277840579338 chr19 59128983 2373349 0.04013850534178814 0.3470312855017059 chr20 63025520 2733935 0.043378222028156214 0.23720697015903094 chr21 48129895 1790902 0.03720976328745367 0.22974915702661736 chr22 51304566 1523307 0.029691450854491198 0.19076902692211525 chrMT 16571 28734 1.7339931205117374 1.5907887191431695 chrX 155270560 6739886 0.04340736582646446 0.2543291209620848 chrY 59373566 327702 0.005519324879357928 0.12973900577128478