BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013353.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 = 3,444,475 number of mapped reads = 3,102,506 (90.07%) number of supplementary alignments = 20,061 (0.58%) number of secondary alignments = 0 number of mapped bases = 201,685,565 bp number of sequenced bases = 201,596,672 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 115,534 duplication rate = 2.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8524 >>>>>>> ACTG content number of A's = 55,211,355 bp (27.39%) number of C's = 38,973,280 bp (19.33%) number of T's = 61,029,511 bp (30.27%) number of G's = 46,338,043 bp (22.99%) number of N's = 44,483 bp (0.02%) GC percentage = 42.32% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,650,381 number of insertions = 14,340 mapped reads with insertion percentage = 0.46% number of deletions = 51,639 mapped reads with deletion percentage = 1.65% homopolymer indels = 44.23% >>>>>>> Coverage mean coverageData = 0.0652X std coverageData = 0.546X There is a 5.48% of reference with a coverageData >= 1X There is a 0.73% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 14942733 0.05995063498758545 0.921074344880208 chr2 243199373 20700176 0.08511607470303799 0.6765471838311922 chr3 198022430 11723952 0.05920517185856168 0.27819198561396064 chr4 191154276 12043847 0.0630058989629926 0.3042522552688051 chr5 180915260 10496338 0.058017980351685094 0.278648065487996 chr6 171115067 10499137 0.06135717435098804 0.39812443659509233 chr7 159138663 13939012 0.0875903550854892 1.124109260973766 chr8 146364022 10928858 0.07466901941243456 0.4645560878696672 chr9 141213431 6958358 0.049275468705239515 0.4087662387245447 chr10 135534747 9383314 0.06923179633042735 0.5396553577823638 chr11 135006516 7968216 0.05902097347656909 0.3772297249400492 chr12 133851895 9911988 0.07405190639998037 0.3186776367864959 chr13 115169878 5584002 0.04848491721073109 0.2581751221844543 chr14 107349540 6767640 0.06304302747827331 0.32709201418024 chr15 102531392 5380243 0.05247410471126736 0.2636573939035188 chr16 90354753 6707042 0.07423009611901656 0.36222642026243534 chr17 81195210 5518921 0.06797101700950094 0.3414625859586832 chr18 78077248 4549616 0.05827070134439165 0.7739414714378858 chr19 59128983 4813934 0.08141411801383426 0.7187364264695401 chr20 63025520 4466385 0.07086629352681263 0.31126428177903437 chr21 48129895 3246821 0.06745954878979063 0.32150016220189825 chr22 51304566 2177088 0.04243458564682138 0.23397313836623715 chrMT 16571 661794 39.93687767787098 24.759572804552498 chrX 155270560 11831019 0.07619615077062902 0.3602192224063461 chrY 59373566 485131 0.008170824706739023 0.15624496161210982