BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038481.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 11,697,270 number of mapped reads = 11,352,386 (97.05%) number of supplementary alignments = 204,119 (1.75%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,759,561 number of mapped paired reads (second in pair) = 5,592,825 number of mapped paired reads (both in pair) = 11,171,780 number of mapped paired reads (singletons) = 180,606 number of mapped bases = 1,606,229,652 bp number of sequenced bases = 1,605,070,959 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,603,719 duplication rate = 8.55% >>>>>>> Insert size mean insert size = 84,610.2526 std insert size = 2,738,930.7433 median insert size = 253 >>>>>>> Mapping quality mean mapping quality = 53.5706 >>>>>>> ACTG content number of A's = 464,551,533 bp (28.94%) number of C's = 329,100,692 bp (20.5%) number of T's = 465,412,374 bp (29%) number of G's = 345,972,467 bp (21.55%) number of N's = 33,893 bp (0%) GC percentage = 42.06% >>>>>>> Mismatches and indels general error rate = 0.0155 number of mismatches = 24,138,383 number of insertions = 286,848 mapped reads with insertion percentage = 2.37% number of deletions = 565,035 mapped reads with deletion percentage = 4.78% homopolymer indels = 46.74% >>>>>>> Coverage mean coverageData = 0.5189X std coverageData = 7.9221X There is a 24.65% of reference with a coverageData >= 1X There is a 11.79% of reference with a coverageData >= 2X There is a 5.38% of reference with a coverageData >= 3X There is a 2.82% of reference with a coverageData >= 4X There is a 1.44% of reference with a coverageData >= 5X There is a 0.79% of reference with a coverageData >= 6X There is a 0.44% of reference with a coverageData >= 7X There is a 0.26% of reference with a coverageData >= 8X There is a 0.16% of reference with a coverageData >= 9X There is a 0.1% of reference with a coverageData >= 10X There is a 0.07% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% 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 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 111622650 0.4478329865424889 10.091298326659292 chr2 243199373 153672518 0.631878758996636 8.650955045152898 chr3 198022430 104324914 0.5268338238249071 1.2172047213193844 chr4 191154276 97224977 0.5086204663295107 6.09158325290601 chr5 180915260 90121591 0.4981425613295418 1.2074108827644914 chr6 171115067 100357010 0.5864884475661047 9.961420791941162 chr7 159138663 104201677 0.6547854244571604 6.792959057185944 chr8 146364022 73457534 0.5018824503196557 2.018995549154018 chr9 141213431 67190316 0.4758068373822034 12.19232911154442 chr10 135534747 77231003 0.569824378688662 19.352784069133758 chr11 135006516 82081265 0.607980025201154 7.044877753317377 chr12 133851895 56331465 0.42084921547057663 1.0622260275598197 chr13 115169878 83320745 0.7234595229839524 1.4664428685195572 chr14 107349540 36473682 0.3397656105466311 1.0525191729383854 chr15 102531392 34527667 0.33675215294063304 0.8965432033664791 chr16 90354753 66016440 0.730636051874327 13.275918775859529 chr17 81195210 41173010 0.5070866865175914 7.564417456065036 chr18 78077248 33362802 0.4273050453827471 11.047427746747065 chr19 59128983 25074631 0.4240666713310459 6.084169175399098 chr20 63025520 45669557 0.7246200745348869 2.3093522071295545 chr21 48129895 16476726 0.34233870653571963 2.6836480452542437 chr22 51304566 13083955 0.25502515702013734 0.8503864010937444 chrMT 16571 2176295 131.33154305714802 94.01429233588071 chrX 155270560 70016860 0.4509345493440611 1.8918600846654 chrY 59373566 21040362 0.3543725502355712 9.219087006224918