BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089591.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 21,778,295 number of mapped reads = 15,291,656 (70.22%) number of supplementary alignments = 605 (0%) number of secondary alignments = 0 number of mapped bases = 721,317,881 bp number of sequenced bases = 721,173,363 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,531,166 duplication rate = 11.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2563 >>>>>>> ACTG content number of A's = 212,299,768 bp (29.44%) number of C's = 149,832,297 bp (20.78%) number of T's = 209,136,852 bp (29%) number of G's = 149,890,966 bp (20.78%) number of N's = 13,480 bp (0%) GC percentage = 41.56% >>>>>>> Mismatches and indels general error rate = 0.0044 number of mismatches = 3,130,089 number of insertions = 28,037 mapped reads with insertion percentage = 0.18% number of deletions = 96,761 mapped reads with deletion percentage = 0.63% homopolymer indels = 46.41% >>>>>>> Coverage mean coverageData = 0.233X std coverageData = 1.2968X There is a 10.51% of reference with a coverageData >= 1X There is a 4.92% of reference with a coverageData >= 2X There is a 2.71% of reference with a coverageData >= 3X There is a 1.62% of reference with a coverageData >= 4X There is a 1.02% of reference with a coverageData >= 5X There is a 0.67% of reference with a coverageData >= 6X There is a 0.45% of reference with a coverageData >= 7X There is a 0.31% of reference with a coverageData >= 8X There is a 0.22% of reference with a coverageData >= 9X There is a 0.16% of reference with a coverageData >= 10X There is a 0.11% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% 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 55786752 0.22381790575358285 1.694282155508085 chr2 243199373 61271094 0.2519377136716549 1.6131474582489622 chr3 198022430 48974008 0.24731545815289713 0.9919452595588535 chr4 191154276 48240774 0.2523656546401295 1.038672782954375 chr5 180915260 42988271 0.23761550573456325 0.9753579688367232 chr6 171115067 44447261 0.25975071499694413 1.204010145572248 chr7 159138663 39391584 0.24752994185957186 1.817105140481841 chr8 146364022 36769160 0.25121720145132387 1.7820146705195203 chr9 141213431 29752381 0.21069087259837205 1.1628754899768576 chr10 135534747 32460155 0.2394969239880604 1.2877738594038222 chr11 135006516 32269976 0.23902532230370274 1.2087411518984472 chr12 133851895 34640370 0.2587962613454221 1.0534960305437786 chr13 115169878 23569522 0.20465005615443996 0.8984782528067681 chr14 107349540 23214094 0.21624772681839158 1.0510546785017103 chr15 102531392 19330746 0.18853490255940347 0.8612259962961564 chr16 90354753 20015587 0.22152223690988343 1.012560771328614 chr17 81195210 17469495 0.21515425602076774 0.9855728651052634 chr18 78077248 19355100 0.24789680087085036 1.818662133368065 chr19 59128983 13128253 0.22202737699716568 1.5892747553954067 chr20 63025520 14413694 0.22869615355811423 1.004799319851332 chr21 48129895 9587595 0.19920249150761704 0.9935235149951784 chr22 51304566 7958095 0.15511475138489622 0.7768202595351826 chrMT 16571 497210 30.004827711061495 23.015336077126978 chrX 155270560 43811163 0.2821601403382586 1.2261955985649282 chrY 59373566 1975541 0.033273073070935306 0.4969280178006446