BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085141.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,435,677 number of mapped reads = 2,220,857 (91.18%) number of supplementary alignments = 22,347 (0.92%) number of secondary alignments = 0 number of mapped bases = 151,433,631 bp number of sequenced bases = 151,379,165 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 83,697 duplication rate = 2.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2028 >>>>>>> ACTG content number of A's = 43,242,509 bp (28.57%) number of C's = 27,979,351 bp (18.48%) number of T's = 47,757,562 bp (31.55%) number of G's = 32,371,369 bp (21.38%) number of N's = 28,374 bp (0.02%) GC percentage = 39.87% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,315,869 number of insertions = 11,845 mapped reads with insertion percentage = 0.53% number of deletions = 33,380 mapped reads with deletion percentage = 1.49% homopolymer indels = 47.85% >>>>>>> Coverage mean coverageData = 0.0489X std coverageData = 0.3959X There is a 4.27% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% 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 11788223 0.04729465849555496 0.6171364508771415 chr2 243199373 12932281 0.05317563462632776 0.4437881970279754 chr3 198022430 10428811 0.0526647966091518 0.25376503727692334 chr4 191154276 10402592 0.05441987601679389 0.26799165692331217 chr5 180915260 9476178 0.052379097263547586 0.2554722709434917 chr6 171115067 8849752 0.05171813420731677 0.28646347411824624 chr7 159138663 8385890 0.05269549110136736 0.4611253431533151 chr8 146364022 7715556 0.05271483998984395 0.807646498596488 chr9 141213431 6352544 0.04498540935529001 0.3552628488739237 chr10 135534747 7295000 0.05382383603814895 0.3531028464937352 chr11 135006516 7118222 0.05272502550913913 0.34519353484267773 chr12 133851895 6754818 0.050464866410744505 0.2527676565050796 chr13 115169878 5169741 0.04488796106912608 0.2358052258360362 chr14 107349540 4529374 0.042192765800393744 0.24212035981376556 chr15 102531392 4347851 0.04240507141461612 0.23377778510553449 chr16 90354753 4040549 0.04471872110590574 0.25821933743220055 chr17 81195210 3569373 0.04396038879633417 0.2584267424259756 chr18 78077248 4162563 0.0533133929105698 0.6593904710819724 chr19 59128983 2551065 0.04314407031150866 0.49864445903057214 chr20 63025520 2931336 0.046510302493339206 0.24517283508001658 chr21 48129895 1977296 0.04108249145359656 0.23879531488141345 chr22 51304566 1562577 0.03045687980286199 0.19177085944298755 chrMT 16571 1800 0.10862349888359182 0.34501000747332794 chrX 155270560 8717367 0.05614307696191732 0.2903512541359523 chrY 59373566 372872 0.006280101148042885 0.14013708809456502