BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506331.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 = 3,509,331 number of mapped reads = 2,341,478 (66.72%) number of supplementary alignments = 35,885 (1.02%) number of secondary alignments = 0 number of mapped bases = 183,242,561 bp number of sequenced bases = 183,165,071 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 177,752 duplication rate = 6.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.0072 >>>>>>> ACTG content number of A's = 49,514,770 bp (27.03%) number of C's = 33,432,087 bp (18.25%) number of T's = 56,255,306 bp (30.71%) number of G's = 43,920,117 bp (23.98%) number of N's = 42,791 bp (0.02%) GC percentage = 42.23% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,442,267 number of insertions = 14,741 mapped reads with insertion percentage = 0.62% number of deletions = 40,179 mapped reads with deletion percentage = 1.69% homopolymer indels = 45.82% >>>>>>> Coverage mean coverageData = 0.0592X std coverageData = 0.4591X There is a 4.62% of reference with a coverageData >= 1X There is a 0.9% of reference with a coverageData >= 2X There is a 0.21% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% 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 13635393 0.054705552769716066 0.765402430829377 chr2 243199373 14979513 0.06159355106561068 0.5016331996832943 chr3 198022430 11913983 0.0601648156726488 0.2986514534893902 chr4 191154276 11693173 0.0611713912170084 0.36574664610536206 chr5 180915260 13938745 0.07704571189848772 0.34356354693735724 chr6 171115067 6877167 0.0401903065613737 0.2854930426248255 chr7 159138663 9310404 0.0585049781397246 0.555608859095919 chr8 146364022 11775979 0.08045678739273782 0.6267604306993164 chr9 141213431 5239070 0.03710036618259066 0.4356739967817477 chr10 135534747 10429963 0.07695416290554628 0.5032235641328735 chr11 135006516 8015575 0.059371763952489526 0.43881376628820734 chr12 133851895 7776298 0.05809628619751704 0.29945833020027607 chr13 115169878 3843262 0.033370374847492675 0.21982339637803305 chr14 107349540 5221644 0.048641512576579275 0.3103209162092687 chr15 102531392 6534562 0.06373230551673384 0.3129046399742051 chr16 90354753 6531004 0.07228179794813894 0.36899279555644954 chr17 81195210 4524771 0.05572706813616222 0.3314887966368362 chr18 78077248 3275927 0.0419575111048996 0.7486166704549531 chr19 59128983 4241472 0.07173253766262139 0.5941029145244582 chr20 63025520 4748553 0.07534333711169698 0.3505818069086341 chr21 48129895 3029368 0.06294150444334026 0.37430632493836646 chr22 51304566 1976073 0.0385165133255391 0.24258573085899326 chrMT 16571 15564 0.9392311870134572 1.2078306516605444 chrX 155270560 13132602 0.08457882807919286 0.4087926635985334 chrY 59373566 582496 0.009810695891164765 0.2926595913113747