BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081956.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 = 3,080,173 number of mapped reads = 2,794,909 (90.74%) number of supplementary alignments = 18,746 (0.61%) number of secondary alignments = 0 number of mapped bases = 194,749,105 bp number of sequenced bases = 194,665,437 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 125,139 duplication rate = 3.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.239 >>>>>>> ACTG content number of A's = 56,880,106 bp (29.22%) number of C's = 36,211,763 bp (18.6%) number of T's = 61,164,380 bp (31.42%) number of G's = 40,383,657 bp (20.75%) number of N's = 25,531 bp (0.01%) GC percentage = 39.35% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,566,835 number of insertions = 14,503 mapped reads with insertion percentage = 0.52% number of deletions = 47,684 mapped reads with deletion percentage = 1.69% homopolymer indels = 47.03% >>>>>>> Coverage mean coverageData = 0.0629X std coverageData = 0.6608X There is a 5.38% of reference with a coverageData >= 1X There is a 0.64% of reference with a coverageData >= 2X There is a 0.09% 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 0.01% 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 18226394 0.07312476866406684 1.35678492324727 chr2 243199373 17431007 0.07167373330358051 0.8001882665258497 chr3 198022430 12582486 0.0635407110194537 0.29269016155518357 chr4 191154276 10419342 0.05450750157427815 0.2843140278105961 chr5 180915260 9974675 0.05513451435771642 0.2694578450783379 chr6 171115067 17223734 0.100655858668483 0.5190054748361009 chr7 159138663 13085819 0.08222903694999624 0.8912567052490175 chr8 146364022 11358888 0.07760710483892004 0.975988728835146 chr9 141213431 9536321 0.06753126053569225 0.6315811537935565 chr10 135534747 8076357 0.05958883001419555 0.7016243940236443 chr11 135006516 8876217 0.06574658218718865 0.419970682322125 chr12 133851895 6549400 0.048930200054321235 0.27395365075791783 chr13 115169878 5392712 0.04682397944365279 0.2391455516951272 chr14 107349540 4861159 0.045283463720477986 0.2909509506722692 chr15 102531392 4394766 0.04286263859560202 0.2316178503073431 chr16 90354753 4148455 0.04591296929338073 0.341604542400563 chr17 81195210 5316526 0.06547832070389374 0.3215296878540332 chr18 78077248 5718487 0.07324140061903821 1.0892191226860328 chr19 59128983 3929888 0.06646297298906696 0.9860890519784795 chr20 63025520 4167863 0.06612976775122205 0.3002995604927172 chr21 48129895 1955295 0.040625374312576415 0.274137757778446 chr22 51304566 1513822 0.029506574522041567 0.18754699017674675 chrMT 16571 3743 0.2258765312896023 0.46138329890822527 chrX 155270560 9579411 0.06169496007485257 0.34644137553608695 chrY 59373566 426338 0.0071806028965819575 0.18490461617271503