BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237302.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,598,730 number of mapped reads = 3,243,822 (90.14%) number of supplementary alignments = 37,735 (1.05%) number of secondary alignments = 0 number of mapped bases = 198,980,109 bp number of sequenced bases = 198,881,772 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,393,264 duplication rate = 21.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 32.2231 >>>>>>> ACTG content number of A's = 49,447,752 bp (24.86%) number of C's = 35,101,855 bp (17.65%) number of T's = 65,904,066 bp (33.14%) number of G's = 48,407,459 bp (24.34%) number of N's = 20,640 bp (0.01%) GC percentage = 41.99% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 1,252,518 number of insertions = 13,466 mapped reads with insertion percentage = 0.41% number of deletions = 57,007 mapped reads with deletion percentage = 1.74% homopolymer indels = 40.52% >>>>>>> Coverage mean coverageData = 0.0643X std coverageData = 1.0326X There is a 1.53% of reference with a coverageData >= 1X There is a 0.94% of reference with a coverageData >= 2X There is a 0.74% of reference with a coverageData >= 3X There is a 0.6% of reference with a coverageData >= 4X There is a 0.49% of reference with a coverageData >= 5X There is a 0.39% of reference with a coverageData >= 6X There is a 0.32% of reference with a coverageData >= 7X There is a 0.25% of reference with a coverageData >= 8X There is a 0.2% of reference with a coverageData >= 9X There is a 0.16% of reference with a coverageData >= 10X There is a 0.13% of reference with a coverageData >= 11X There is a 0.11% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% 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% 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 7821273 0.031379151508713794 0.7078828304915689 chr2 243199373 6882610 0.02830027855376091 2.045739950585726 chr3 198022430 2009061 0.010145623402359015 0.250462732955431 chr4 191154276 2673691 0.013987084442725204 0.3445440609481029 chr5 180915260 3720611 0.020565490163737432 0.41872165241254794 chr6 171115067 4058558 0.023718297115238835 0.6983258194905231 chr7 159138663 7482252 0.04701718525811669 0.6863209562388832 chr8 146364022 38932688 0.2659990308273983 1.6387180145548221 chr9 141213431 1890322 0.013386276267163284 0.4196162238988476 chr10 135534747 25103427 0.1852176475453929 1.3097657889687677 chr11 135006516 4820578 0.03570626176295076 0.7659861595526363 chr12 133851895 3972706 0.029679863703087655 0.5037405350021085 chr13 115169878 1065006 0.009247261684170578 0.39339727661618007 chr14 107349540 13785145 0.12841363828852922 1.0858257458904252 chr15 102531392 2037033 0.019867408022705865 0.4510420844696482 chr16 90354753 9715315 0.10752411663390857 1.0189752958579645 chr17 81195210 13657138 0.1682012768979845 1.6510695889880145 chr18 78077248 6221560 0.0796846733122561 1.8312943504373362 chr19 59128983 2688399 0.045466687631004914 0.649387396225077 chr20 63025520 2509517 0.03981747393754149 0.5799518318943732 chr21 48129895 3534122 0.07342883253744892 0.8241052546703903 chr22 51304566 4326286 0.08432555496132645 0.865058085381426 chrMT 16571 4454 0.2687828133486211 1.0153721304683525 chrX 155270560 29057900 0.18714365427676696 1.352182664357646 chrY 59373566 1010457 0.017018634184781826 0.42228468800255115