BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2971280.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 11,683,360 number of mapped reads = 8,538,630 (73.08%) number of secondary alignments = 0 number of mapped bases = 336,982,390 bp number of sequenced bases = 336,948,714 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 672,090 duplication rate = 6.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1639 >>>>>>> ACTG content number of A's = 95,895,476 bp (28.46%) number of C's = 70,555,488 bp (20.94%) number of T's = 97,841,045 bp (29.04%) number of G's = 72,653,820 bp (21.56%) number of N's = 2,885 bp (0%) GC percentage = 42.5% >>>>>>> Mismatches and indels general error rate = 0.0027 number of mismatches = 885,299 number of insertions = 10,973 mapped reads with insertion percentage = 0.13% number of deletions = 26,263 mapped reads with deletion percentage = 0.31% homopolymer indels = 39.47% >>>>>>> Coverage mean coverageData = 0.1089X std coverageData = 1.2338X There is a 7.36% of reference with a coverageData >= 1X There is a 2.21% of reference with a coverageData >= 2X There is a 0.73% of reference with a coverageData >= 3X There is a 0.26% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% 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 27302503 0.10953835497164117 1.5206957729464754 chr2 243199373 28501398 0.11719355049488553 0.5837103984008755 chr3 198022430 23137445 0.11684254657414314 0.47190554123552003 chr4 191154276 21113031 0.11045021561537027 0.5025532613343526 chr5 180915260 20640153 0.11408740755202187 0.47144609420524425 chr6 171115067 19304581 0.11281637168747975 0.4790815008368532 chr7 159138663 18070751 0.11355349265439034 0.8101754840109955 chr8 146364022 17845474 0.12192527751116322 4.70358736600383 chr9 141213431 14295945 0.10123643975479925 0.5555263450448837 chr10 135534747 16286930 0.12016793007331175 0.6627882495547887 chr11 135006516 15483178 0.11468467196057411 0.5544954206493916 chr12 133851895 15268622 0.11407101856869489 0.4825924578093049 chr13 115169878 10012988 0.08694103157771861 0.40693644598154516 chr14 107349540 10336578 0.09628898270081082 0.48529853604628675 chr15 102531392 10047391 0.0979933150619861 0.42780037041979346 chr16 90354753 9722580 0.10760452192260433 0.4827054320739868 chr17 81195210 9061314 0.11159912019440556 0.5006481729810236 chr18 78077248 8486120 0.10868876935826427 0.8836317010883885 chr19 59128983 6664790 0.11271612772369179 1.3638169935596136 chr20 63025520 7639192 0.12120791704693591 0.5134122383143296 chr21 48129895 4193715 0.0871332671720975 0.47398919581127735 chr22 51304566 4112840 0.08016518451788482 0.41547779728802975 chrMT 16571 35925 2.167943998551687 2.825562553654747 chrX 155270560 18339567 0.1181136140682432 0.5403428404223107 chrY 59373566 1079379 0.01817945379935576 0.288062429150036