BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506125.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 8,656,556 number of mapped reads = 6,575,107 (75.96%) number of supplementary alignments = 102,803 (1.19%) number of secondary alignments = 0 number of mapped bases = 517,566,018 bp number of sequenced bases = 517,333,845 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,129,026 duplication rate = 11.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6649 >>>>>>> ACTG content number of A's = 141,638,867 bp (27.38%) number of C's = 99,550,806 bp (19.24%) number of T's = 141,980,295 bp (27.44%) number of G's = 134,073,850 bp (25.92%) number of N's = 90,027 bp (0.02%) GC percentage = 45.16% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 3,940,286 number of insertions = 49,327 mapped reads with insertion percentage = 0.73% number of deletions = 106,019 mapped reads with deletion percentage = 1.57% homopolymer indels = 40.46% >>>>>>> Coverage mean coverageData = 0.1672X std coverageData = 1.2111X There is a 9.18% of reference with a coverageData >= 1X There is a 3.47% of reference with a coverageData >= 2X There is a 1.59% of reference with a coverageData >= 3X There is a 0.81% of reference with a coverageData >= 4X There is a 0.45% of reference with a coverageData >= 5X There is a 0.27% of reference with a coverageData >= 6X There is a 0.17% of reference with a coverageData >= 7X There is a 0.11% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% 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 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% 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 38813719 0.15572165414986067 1.6941862803216614 chr2 243199373 43022464 0.17690203502292745 1.4160411646554234 chr3 198022430 34386663 0.1736503435494656 0.6991976750295039 chr4 191154276 29965883 0.15676281811242349 1.5345227175206475 chr5 180915260 37377902 0.20660447327660475 0.7787453285529747 chr6 171115067 17842495 0.10427191078387037 0.5759412499187154 chr7 159138663 27245956 0.1712089035208245 1.332285687484707 chr8 146364022 32523317 0.22220841266578475 1.2105538948376438 chr9 141213431 15409763 0.10912391895640579 1.0916870320952867 chr10 135534747 30047528 0.22169612343025216 2.0335463928002606 chr11 135006516 22541329 0.16696474857554283 1.0973433126519687 chr12 133851895 22449546 0.16771929900581534 0.7174388838837881 chr13 115169878 10273102 0.08919955615477859 0.49081554052133297 chr14 107349540 12663977 0.11796955068461402 0.6795340284284841 chr15 102531392 18230447 0.17780356478530984 0.7318695195518593 chr16 90354753 20523255 0.22714084559558256 1.0989056972934608 chr17 81195210 13079257 0.16108409597068596 0.887501888149412 chr18 78077248 9630759 0.12334910933336175 1.6774598190789531 chr19 59128983 13047065 0.22065431093242377 1.3971901962273794 chr20 63025520 14664095 0.23266916322150138 0.9765127627609625 chr21 48129895 7977033 0.16573967177780047 1.2079937828286895 chr22 51304566 6309542 0.12298207531859835 0.7016562176472996 chrMT 16571 99289 5.991732544807193 6.436004379892206 chrX 155270560 36847879 0.23731400852808157 0.9563318522744582 chrY 59373566 2593753 0.04368531612199274 1.933381134556616