BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240210.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 = 3,585,392 number of mapped reads = 2,676,897 (74.66%) number of supplementary alignments = 20,337 (0.57%) number of secondary alignments = 0 number of mapped bases = 170,469,806 bp number of sequenced bases = 170,396,962 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 247,704 duplication rate = 7.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4215 >>>>>>> ACTG content number of A's = 45,472,044 bp (26.69%) number of C's = 31,887,677 bp (18.71%) number of T's = 53,430,199 bp (31.36%) number of G's = 39,591,297 bp (23.23%) number of N's = 15,745 bp (0.01%) GC percentage = 41.95% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,420,005 number of insertions = 11,086 mapped reads with insertion percentage = 0.41% number of deletions = 41,722 mapped reads with deletion percentage = 1.54% homopolymer indels = 46.32% >>>>>>> Coverage mean coverageData = 0.0551X std coverageData = 0.4861X There is a 3.81% of reference with a coverageData >= 1X There is a 1.07% of reference with a coverageData >= 2X There is a 0.34% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% 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 0.01% 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 13508457 0.05419628222310427 0.8647583851777324 chr2 243199373 14083048 0.05790741902940679 0.5795234394585345 chr3 198022430 11684693 0.05900691653970715 0.33227363255672043 chr4 191154276 10822716 0.05661770286530237 0.3445637713015702 chr5 180915260 9698795 0.053609601533889405 0.3176129497654871 chr6 171115067 10734913 0.0627350541843285 0.39908100506323124 chr7 159138663 9420124 0.05919443975723235 0.6110611439001788 chr8 146364022 9202540 0.06287433123421547 0.5280752952874236 chr9 141213431 7597197 0.053799393911759 0.4601883532079994 chr10 135534747 8151359 0.06014220840357639 0.46449243164990694 chr11 135006516 8190100 0.06066447933520483 0.47523507206497306 chr12 133851895 7739318 0.05782001069166783 0.33762330431758253 chr13 115169878 5157696 0.04478337643111856 0.2885151608078146 chr14 107349540 5342477 0.04976711590939281 0.3463801788468621 chr15 102531392 4712385 0.045960411812218445 0.3093523230803742 chr16 90354753 4462576 0.04938949918882519 0.3464245751900165 chr17 81195210 4410089 0.05431464491562987 0.36543049859284243 chr18 78077248 4431462 0.056757405179035 0.8114882920284087 chr19 59128983 3127951 0.05290047014676373 0.584861342608528 chr20 63025520 2879747 0.04569176105171365 0.30657568682345 chr21 48129895 2241703 0.04657610410328134 0.31838559303231756 chr22 51304566 1707605 0.033283684730906794 0.24674113333480208 chrMT 16571 126952 7.661094683483194 5.641732807934259 chrX 155270560 10580985 0.06814546814283404 0.4029618403257665 chrY 59373566 454918 0.007661961890582755 0.16374391696266885