BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549073.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 = 9,447,076 number of mapped reads = 8,175,440 (86.54%) number of secondary alignments = 0 number of mapped bases = 324,950,149 bp number of sequenced bases = 324,917,913 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 296,274 duplication rate = 2.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5229 >>>>>>> ACTG content number of A's = 95,937,993 bp (29.53%) number of C's = 66,476,250 bp (20.46%) number of T's = 96,181,365 bp (29.6%) number of G's = 66,316,327 bp (20.41%) number of N's = 5,978 bp (0%) GC percentage = 40.87% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 973,730 number of insertions = 7,745 mapped reads with insertion percentage = 0.09% number of deletions = 25,326 mapped reads with deletion percentage = 0.31% homopolymer indels = 44.93% >>>>>>> Coverage mean coverageData = 0.105X std coverageData = 0.8989X There is a 8.61% of reference with a coverageData >= 1X There is a 1.4% of reference with a coverageData >= 2X There is a 0.25% of reference with a coverageData >= 3X There is a 0.05% 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 0.01% 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 26636023 0.10686441980820581 1.9396342420493398 chr2 243199373 28077014 0.1154485459960458 0.5653377295566325 chr3 198022430 22592046 0.11408831817688532 0.39722113414042587 chr4 191154276 22125607 0.11574738197329157 0.43186930731704093 chr5 180915260 20547468 0.1135750958763788 0.39967672675409643 chr6 171115067 19465476 0.1137566454039959 0.4620180496458666 chr7 159138663 18207566 0.11441321459386648 0.8203586407201463 chr8 146364022 17170616 0.11731445860376807 2.2719080143369497 chr9 141213431 13797220 0.097704728950322 0.5183914761991325 chr10 135534747 15469696 0.114138229069775 0.6278848504611381 chr11 135006516 15114593 0.11195454447546813 0.5595648936981014 chr12 133851895 15071661 0.11259953398493162 0.40595477106785355 chr13 115169878 10920629 0.09482192036358673 0.35235133701706695 chr14 107349540 10072155 0.09382578630518584 0.40092009437966103 chr15 102531392 9426202 0.09193479007873023 0.34833701137304945 chr16 90354753 8905166 0.0985578035944606 0.41628400276274075 chr17 81195210 8377594 0.10317842641209993 0.40957939990459485 chr18 78077248 8912956 0.11415561163221327 1.0580309524475289 chr19 59128983 5895901 0.09971253860395332 1.3650377019232296 chr20 63025520 6804655 0.10796666175860191 0.39850555602396553 chr21 48129895 4290074 0.08913532846892767 0.41516287885489844 chr22 51304566 3605098 0.07026856050200288 0.34046111044088595 chrMT 16571 10554 0.63689578178746 1.0755707546198623 chrX 155270560 10545004 0.06791373715661231 0.38479933461804317 chrY 59373566 2909175 0.04899781495354347 0.5260530808497412