BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230358.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,879,205 number of mapped reads = 2,638,231 (91.63%) number of supplementary alignments = 22,100 (0.77%) number of secondary alignments = 0 number of mapped bases = 185,720,559 bp number of sequenced bases = 185,643,818 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 135,210 duplication rate = 3.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.0958 >>>>>>> ACTG content number of A's = 56,203,385 bp (30.27%) number of C's = 37,524,898 bp (20.21%) number of T's = 54,455,468 bp (29.33%) number of G's = 37,379,603 bp (20.14%) number of N's = 80,464 bp (0.04%) GC percentage = 40.35% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,539,122 number of insertions = 15,066 mapped reads with insertion percentage = 0.57% number of deletions = 45,619 mapped reads with deletion percentage = 1.71% homopolymer indels = 46.59% >>>>>>> Coverage mean coverageData = 0.06X std coverageData = 0.6921X There is a 3.06% of reference with a coverageData >= 1X There is a 1.36% of reference with a coverageData >= 2X There is a 0.68% of reference with a coverageData >= 3X There is a 0.35% of reference with a coverageData >= 4X There is a 0.18% of reference with a coverageData >= 5X There is a 0.1% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% 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% 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 26891037 0.10788754263524984 0.7680910191251972 chr2 243199373 47945992 0.1971468569534511 0.9058210961109341 chr3 198022430 4683641 0.02365207315151117 0.344990840731701 chr4 191154276 8764574 0.04585078703654006 0.4110381093200952 chr5 180915260 1372509 0.007586474463237651 0.15495380937372252 chr6 171115067 8438111 0.04931249566702387 0.48299965909630127 chr7 159138663 22321666 0.14026551171917287 1.8461485289415673 chr8 146364022 969898 0.006626614838447115 0.16602332199903688 chr9 141213431 7699694 0.054525224303912 0.5749822881358607 chr10 135534747 13355528 0.09853951326592288 1.1644797863198626 chr11 135006516 1044871 0.007739411629583864 0.2416794100112173 chr12 133851895 13218256 0.09875284918454087 0.5492684927487829 chr13 115169878 490584 0.004259655463036958 0.0961837448911103 chr14 107349540 7041411 0.06559330389305813 0.46029636249006933 chr15 102531392 6703697 0.06538189786792323 0.43644829917579486 chr16 90354753 658527 0.007288238616511961 0.2833017964339856 chr17 81195210 777735 0.00957858228336376 0.17249829346640416 chr18 78077248 9328892 0.11948284857581046 1.2608926772024498 chr19 59128983 1300156 0.02198847221843812 0.42779743215634236 chr20 63025520 498243 0.007905416726430817 0.14762754990582683 chr21 48129895 435551 0.009049489927206365 0.242403800135853 chr22 51304566 293700 0.005724636672689133 0.10995324254298403 chrMT 16571 10710 0.6463098183573713 1.172275499818057 chrX 155270560 1121623 0.00722366815705437 0.1636800208978844 chrY 59373566 353953 0.005961457662825911 0.25039134937143503