BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084811.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 = 2,380,320 number of mapped reads = 2,175,077 (91.38%) number of supplementary alignments = 21,917 (0.92%) number of secondary alignments = 0 number of mapped bases = 146,235,607 bp number of sequenced bases = 146,179,375 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 97,175 duplication rate = 3.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7216 >>>>>>> ACTG content number of A's = 39,904,122 bp (27.3%) number of C's = 27,768,458 bp (19%) number of T's = 45,444,795 bp (31.09%) number of G's = 33,041,826 bp (22.6%) number of N's = 20,174 bp (0.01%) GC percentage = 41.6% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,118,075 number of insertions = 11,532 mapped reads with insertion percentage = 0.53% number of deletions = 34,065 mapped reads with deletion percentage = 1.55% homopolymer indels = 48.21% >>>>>>> Coverage mean coverageData = 0.0472X std coverageData = 0.3226X There is a 3.92% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.11% 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% 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 12181179 0.04887120822860457 0.4177750955556672 chr2 243199373 12981725 0.053378941071529816 0.5112965310837618 chr3 198022430 9524313 0.048097142328775586 0.25550882898186267 chr4 191154276 9135577 0.04779164343673902 0.2603591291482852 chr5 180915260 8459680 0.046760455696219325 0.25378976539056974 chr6 171115067 7607482 0.04445828256608169 0.2671368537993582 chr7 159138663 8929169 0.056109362939664766 0.3421522725745407 chr8 146364022 8055662 0.05503853945746312 0.3268104942925637 chr9 141213431 9729212 0.06889721417504543 0.3720655590801537 chr10 135534747 5376786 0.03967090446555377 0.26156732431227225 chr11 135006516 6242281 0.04623688681811476 0.30941878795945144 chr12 133851895 5631988 0.042076266458536134 0.24157677050385895 chr13 115169878 4687762 0.040703021322988635 0.23492931560615773 chr14 107349540 3071629 0.028613341053906706 0.20864288735580774 chr15 102531392 4601781 0.04488167877404805 0.25767241205488867 chr16 90354753 2949110 0.03263923481701068 0.22044491720642773 chr17 81195210 5375291 0.06620207029454077 0.31197456176032984 chr18 78077248 5010347 0.06417166496442088 0.5138934107290802 chr19 59128983 2852487 0.04824177341254119 0.35517805596173235 chr20 63025520 2856064 0.04531599263282556 0.2551472672002213 chr21 48129895 1557255 0.03235525446294865 0.21608532600419542 chr22 51304566 1540176 0.03002025199862328 0.20013594240511456 chrMT 16571 189026 11.407036388872125 6.1233541051871585 chrX 155270560 7404029 0.04768469309314013 0.26999928267704054 chrY 59373566 285596 0.0048101540675525535 0.09108986923845688