BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240220.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 = 2,784,816 number of mapped reads = 2,344,611 (84.19%) number of supplementary alignments = 20,426 (0.73%) number of secondary alignments = 0 number of mapped bases = 158,437,468 bp number of sequenced bases = 158,372,228 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 139,695 duplication rate = 4.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0473 >>>>>>> ACTG content number of A's = 45,491,804 bp (28.72%) number of C's = 29,827,147 bp (18.83%) number of T's = 49,788,932 bp (31.44%) number of G's = 33,249,887 bp (20.99%) number of N's = 14,458 bp (0.01%) GC percentage = 39.83% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,249,619 number of insertions = 11,913 mapped reads with insertion percentage = 0.5% number of deletions = 36,816 mapped reads with deletion percentage = 1.55% homopolymer indels = 47.29% >>>>>>> Coverage mean coverageData = 0.0512X std coverageData = 0.5303X There is a 3.66% of reference with a coverageData >= 1X There is a 0.95% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.03% 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 17673749 0.07090754249314388 1.0021527484572952 chr2 243199373 11985754 0.04928365501994941 0.4680729985603449 chr3 198022430 10224112 0.05163108037811676 0.3039749586405786 chr4 191154276 9134615 0.047786610852482314 0.3023284707743468 chr5 180915260 11618857 0.06422264766388419 0.3369918953830717 chr6 171115067 9982172 0.058336020170567444 0.34238715289138527 chr7 159138663 8251407 0.051850423048985905 0.476249025307346 chr8 146364022 6879186 0.04700052585327288 1.1816330319993193 chr9 141213431 6326499 0.044800972224802046 0.4487734483350769 chr10 135534747 8596943 0.0634298081509681 0.4474748711018702 chr11 135006516 6580957 0.048745476847947104 0.4451987347684226 chr12 133851895 5691695 0.04252233410666319 0.2784310352770347 chr13 115169878 4829077 0.0419300348655401 0.27100422236685645 chr14 107349540 4237704 0.0394757536920978 0.29180935740764763 chr15 102531392 4458409 0.043483355809701675 0.27881636616617844 chr16 90354753 3888059 0.043031040104774564 0.31101611916180444 chr17 81195210 3243714 0.039949573380006036 0.2913969772865353 chr18 78077248 3884093 0.04974679691579293 0.8657219612450142 chr19 59128983 3120342 0.05277178536962153 0.5893559091257 chr20 63025520 3957122 0.06278602699350994 0.34194235837865816 chr21 48129895 2462056 0.05115440206133839 0.3183731480489689 chr22 51304566 1535285 0.029924919353181936 0.22318826742189887 chrMT 16571 25103 1.5148753847082252 1.8197587903032744 chrX 155270560 9408661 0.06059526673955449 0.3604612221543897 chrY 59373566 441897 0.007442655541356569 0.16424027003856848