BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818914.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 3,255,833 number of mapped reads = 2,886,623 (88.66%) number of supplementary alignments = 37,407 (1.15%) number of secondary alignments = 0 number of mapped bases = 267,699,372 bp number of sequenced bases = 267,528,806 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 826,467 duplication rate = 23.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2604 >>>>>>> ACTG content number of A's = 78,662,350 bp (29.4%) number of C's = 54,826,968 bp (20.49%) number of T's = 74,937,888 bp (28.01%) number of G's = 59,097,799 bp (22.09%) number of N's = 3,801 bp (0%) GC percentage = 42.58% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 1,596,743 number of insertions = 39,493 mapped reads with insertion percentage = 1.32% number of deletions = 85,580 mapped reads with deletion percentage = 2.89% homopolymer indels = 41.2% >>>>>>> Coverage mean coverageData = 0.0865X std coverageData = 1.1377X There is a 5.28% of reference with a coverageData >= 1X There is a 1.76% of reference with a coverageData >= 2X There is a 0.69% of reference with a coverageData >= 3X There is a 0.3% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% 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 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 24945402 0.10008160420992492 1.9225234017730575 chr2 243199373 19495530 0.0801627477880052 1.547075718198245 chr3 198022430 15688319 0.07922495951594978 0.41990980286002627 chr4 191154276 15441319 0.08077935436819629 0.607656940507312 chr5 180915260 13970932 0.07722362392205058 0.446294363176309 chr6 171115067 12588525 0.07356760115110143 0.47042594801429294 chr7 159138663 23075360 0.14500159524401685 2.56090036261608 chr8 146364022 23982421 0.1638546185892596 0.8467706471455155 chr9 141213431 9603275 0.06800539390619297 0.9068141527956449 chr10 135534747 12119634 0.08942086268106583 1.45879373376202 chr11 135006516 11235806 0.08322417563904841 0.5990480060204668 chr12 133851895 10021956 0.07487347116004596 0.4184606156845977 chr13 115169878 6324851 0.05491758009850457 0.3402818881261006 chr14 107349540 8727903 0.08130359012251007 0.48708688442970116 chr15 102531392 7255627 0.07076493216828657 0.39377604290543383 chr16 90354753 6688270 0.07402233726431635 1.0966445917784766 chr17 81195210 7046950 0.08679021828997055 0.6500694094902512 chr18 78077248 4694459 0.06012582564385466 1.0784201281773116 chr19 59128983 5381973 0.09102089579318487 1.8100641903166568 chr20 63025520 10807199 0.17147338094156145 0.6947535358056877 chr21 48129895 3326814 0.06912157194608465 0.4785436782392674 chr22 51304566 3197093 0.06231595449028845 0.4221768326581494 chrMT 16571 555926 33.54812624464426 21.53183220371043 chrX 155270560 10526408 0.06779397201890687 0.5044392829099321 chrY 59373566 997420 0.016799058355363057 1.2832352341392745