BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004055.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 = 2,296,279 number of mapped reads = 2,032,372 (88.51%) number of supplementary alignments = 12,273 (0.53%) number of secondary alignments = 0 number of mapped bases = 134,689,034 bp number of sequenced bases = 134,634,595 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 72,625 duplication rate = 2.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4582 >>>>>>> ACTG content number of A's = 37,199,798 bp (27.63%) number of C's = 25,587,610 bp (19.01%) number of T's = 41,429,073 bp (30.77%) number of G's = 30,394,298 bp (22.58%) number of N's = 23,816 bp (0.02%) GC percentage = 41.58% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,160,905 number of insertions = 9,759 mapped reads with insertion percentage = 0.48% number of deletions = 31,551 mapped reads with deletion percentage = 1.54% homopolymer indels = 46.48% >>>>>>> Coverage mean coverageData = 0.0435X std coverageData = 0.3568X There is a 3.76% of reference with a coverageData >= 1X There is a 0.44% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% 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 10517448 0.04219627601248785 0.5752133490096533 chr2 243199373 10246335 0.042131420297699534 0.44880887865611485 chr3 198022430 8904727 0.04496827455354426 0.23651808272840366 chr4 191154276 8940407 0.046770635672309 0.2530076345739398 chr5 180915260 7375195 0.04076601940599151 0.2268550530041421 chr6 171115067 8213468 0.04799967731655097 0.27190054051168033 chr7 159138663 8457119 0.05314308189204782 0.5449801455768929 chr8 146364022 8832790 0.060348095654272196 0.472469583238485 chr9 141213431 4019920 0.028466980594784926 0.3237451803351934 chr10 135534747 6885186 0.05080015385279762 0.3144877895665006 chr11 135006516 5721010 0.04237580651292416 0.3146145543334564 chr12 133851895 6263202 0.046792030848722764 0.24776958986761627 chr13 115169878 4300402 0.037339641881013366 0.22687607506885304 chr14 107349540 3460931 0.03223983074356909 0.22016502076535233 chr15 102531392 3830617 0.03736043103754994 0.23014084231978638 chr16 90354753 3393898 0.0375619199578798 0.23644342644605718 chr17 81195210 3207554 0.03950422691190773 0.24236153186703874 chr18 78077248 4674643 0.05987202571484077 0.5865850099102142 chr19 59128983 2299825 0.038895054224085 0.4364676756321846 chr20 63025520 3230209 0.05125239744154431 0.2710280253758377 chr21 48129895 1448493 0.03009549470240897 0.206570608871513 chr22 51304566 1500834 0.02925341966638993 0.1909453592368151 chrMT 16571 70274 4.240782089191962 3.785098630247891 chrX 155270560 8568363 0.05518343593273574 0.29040261937381284 chrY 59373566 326184 0.0054937579460866475 0.10126123255191863