BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714187.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 41,548 number of mapped reads = 26,162 (62.97%) number of supplementary alignments = 913 (2.2%) number of secondary alignments = 0 number of mapped bases = 3,368,399 bp number of sequenced bases = 3,292,564 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,096 duplication rate = 39.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.9635 >>>>>>> ACTG content number of A's = 895,687 bp (27.2%) number of C's = 672,984 bp (20.44%) number of T's = 849,936 bp (25.81%) number of G's = 873,895 bp (26.54%) number of N's = 62 bp (0%) GC percentage = 46.98% >>>>>>> Mismatches and indels general error rate = 0.0464 number of mismatches = 143,313 number of insertions = 3,569 mapped reads with insertion percentage = 12.98% number of deletions = 12,549 mapped reads with deletion percentage = 43.83% homopolymer indels = 30.93% >>>>>>> Coverage mean coverageData = 0.0011X std coverageData = 0.3048X There is a 0.01% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 230143 9.233397256009244E-4 0.17469684716779973 chr2 243199373 441264 0.0018144125725192556 0.7833093058081169 chr3 198022430 129258 6.527442371048573E-4 0.1115302226146162 chr4 191154276 103524 5.415730276418196E-4 0.1024951251791907 chr5 180915260 198672 0.0010981494872240186 0.17369501474321267 chr6 171115067 133133 7.780320128092519E-4 0.1858350340683039 chr7 159138663 146532 9.207818969799942E-4 0.1731682891642501 chr8 146364022 193894 0.0013247381245098608 0.34793629294135336 chr9 141213431 120825 8.556197462548728E-4 0.1687763671819457 chr10 135534747 117030 8.63468612960188E-4 0.13718053056064752 chr11 135006516 188507 0.0013962807543304058 0.32919234292206107 chr12 133851895 184188 0.001376058217181012 0.3236736040919304 chr13 115169878 93518 8.120005128424291E-4 0.1692193845423401 chr14 107349540 120475 0.0011222684326360412 0.24629692025108663 chr15 102531392 119834 0.0011687542484549512 0.21476810186081705 chr16 90354753 68435 7.574034317818344E-4 0.13266898795429316 chr17 81195210 94628 0.0011654382075001715 0.21363525016044466 chr18 78077248 54787 7.017024985306859E-4 0.12787425314273787 chr19 59128983 61360 0.0010377313609469657 0.17255941979814615 chr20 63025520 63544 0.001008226508880847 0.18895492694769309 chr21 48129895 32769 6.808450340479654E-4 0.12494802983502756 chr22 51304566 28600 5.574552565165448E-4 0.11331106188971381 chrMT 16571 27818 1.678715828857643 12.115427045039718 chrX 155270560 399098 0.002570339155085162 0.42193258528946787 chrY 59373566 16563 2.78962526859175E-4 0.09803030120131877