BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549155.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 13,265,329 number of mapped reads = 11,631,909 (87.69%) number of secondary alignments = 0 number of mapped bases = 461,703,312 bp number of sequenced bases = 461,660,125 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 694,854 duplication rate = 4.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.7188 >>>>>>> ACTG content number of A's = 130,855,102 bp (28.34%) number of C's = 98,447,420 bp (21.32%) number of T's = 133,127,869 bp (28.84%) number of G's = 99,139,189 bp (21.47%) number of N's = 90,545 bp (0.02%) GC percentage = 42.8% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 1,422,492 number of insertions = 11,573 mapped reads with insertion percentage = 0.1% number of deletions = 34,676 mapped reads with deletion percentage = 0.3% homopolymer indels = 46.23% >>>>>>> Coverage mean coverageData = 0.1491X std coverageData = 0.8132X There is a 10.01% of reference with a coverageData >= 1X There is a 3.01% of reference with a coverageData >= 2X There is a 1.03% of reference with a coverageData >= 3X There is a 0.38% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 38722694 0.15535645947297358 1.3537525066752214 chr2 243199373 39457796 0.16224464526066026 0.8536915905487559 chr3 198022430 31530679 0.15922781575804318 0.5561671670157204 chr4 191154276 29142593 0.15245587809921657 0.5567177855674926 chr5 180915260 27778497 0.15354424496861127 0.5577326644526621 chr6 171115067 26955062 0.15752594130124145 0.6326659437928507 chr7 159138663 25873109 0.1625821689855469 1.2495749290292884 chr8 146364022 23563914 0.16099526152677057 0.7627418645563955 chr9 141213431 20066822 0.14210278624276185 0.8244434467046642 chr10 135534747 22092861 0.16300514435608163 0.740115458109654 chr11 135006516 21360591 0.15821896329803814 0.7297517370920594 chr12 133851895 21410767 0.15995863936031687 0.5818511899903083 chr13 115169878 14742936 0.12801034659427182 0.4922003448929107 chr14 107349540 14426441 0.13438754371933034 0.6615369074908884 chr15 102531392 14018082 0.13671990330532136 0.5158582873667813 chr16 90354753 13861936 0.15341678815723175 0.6053456610753883 chr17 81195210 13133130 0.16174759570176614 0.6154940801219728 chr18 78077248 12227356 0.15660587832194087 1.5442662583728932 chr19 59128983 9856510 0.1666950706728712 1.2086215459749186 chr20 63025520 10535521 0.16716277787156694 0.607762449079323 chr21 48129895 6114236 0.12703613835018754 0.583058889535362 chr22 51304566 6110841 0.11910910619534332 0.5154360485430105 chrMT 16571 16280 0.9824392010138193 1.6593971938566614 chrX 155270560 15456717 0.09954699074956644 0.5391016009677707 chrY 59373566 3247941 0.054703485386072316 0.38093193471851833