BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506336.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 = 13,367,703 number of mapped reads = 10,589,518 (79.22%) number of supplementary alignments = 184,991 (1.38%) number of secondary alignments = 0 number of mapped bases = 818,930,313 bp number of sequenced bases = 818,582,888 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,530,899 duplication rate = 10.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5031 >>>>>>> ACTG content number of A's = 230,625,119 bp (28.17%) number of C's = 148,115,240 bp (18.09%) number of T's = 236,742,694 bp (28.92%) number of G's = 202,920,693 bp (24.79%) number of N's = 179,142 bp (0.02%) GC percentage = 42.88% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 6,091,338 number of insertions = 67,565 mapped reads with insertion percentage = 0.62% number of deletions = 177,045 mapped reads with deletion percentage = 1.64% homopolymer indels = 43.93% >>>>>>> Coverage mean coverageData = 0.2645X std coverageData = 1.6186X There is a 15.32% of reference with a coverageData >= 1X There is a 5.67% of reference with a coverageData >= 2X There is a 2.41% of reference with a coverageData >= 3X There is a 1.13% of reference with a coverageData >= 4X There is a 0.57% of reference with a coverageData >= 5X There is a 0.31% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.11% of reference with a coverageData >= 8X There is a 0.07% 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 0.02% 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 0.01% 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 0.01% of reference with a coverageData >= 31X There is a 0.01% 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 60778405 0.24384454793394478 2.813162420889401 chr2 243199373 65773240 0.27044987488516264 1.7617702375276945 chr3 198022430 52959234 0.26744058236231116 0.8079215641405272 chr4 191154276 50166467 0.26243967987407196 1.4299776704718563 chr5 180915260 62251926 0.3440943898264856 0.9482362480789347 chr6 171115067 31023104 0.18129966310915216 0.7972551739777617 chr7 159138663 43547040 0.2736421129791696 1.9260714685405949 chr8 146364022 51689129 0.3531546092659301 2.681885227551573 chr9 141213431 23067455 0.1633517069633412 1.4593451414565939 chr10 135534747 46363265 0.34207659678591495 1.8957268193402104 chr11 135006516 34939594 0.25879931602708717 1.4900331243677767 chr12 133851895 34862897 0.26045874808122815 0.9380672459649466 chr13 115169878 17759568 0.15420323706516387 0.5942703492507976 chr14 107349540 23887198 0.22251793533535402 0.8614393190117705 chr15 102531392 29586117 0.2885566695515067 0.8964085631276334 chr16 90354753 27791414 0.30758109648089016 1.2099106907441781 chr17 81195210 20450321 0.2518661014609113 0.983789429939448 chr18 78077248 14664880 0.18782526761189125 2.5554376599822297 chr19 59128983 19513824 0.3300213027509707 2.06339604463624 chr20 63025520 22035292 0.3496249138444237 1.0516255311236349 chr21 48129895 13472175 0.27991282756798036 1.2560910145037332 chr22 51304566 9652469 0.18814054483961526 0.7104487446527817 chrMT 16571 120803 7.29002474201919 5.619757697181816 chrX 155270560 59657553 0.38421676974695007 1.1992055871077396 chrY 59373566 2916943 0.04912864758704236 1.6273784814584793