BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063525.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 = 4,950,596 number of mapped reads = 4,528,726 (91.48%) number of supplementary alignments = 31,580 (0.64%) number of secondary alignments = 0 number of mapped bases = 290,233,229 bp number of sequenced bases = 290,101,812 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 611,389 duplication rate = 11.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5949 >>>>>>> ACTG content number of A's = 74,499,206 bp (25.68%) number of C's = 52,066,002 bp (17.95%) number of T's = 94,738,570 bp (32.66%) number of G's = 68,765,592 bp (23.7%) number of N's = 32,442 bp (0.01%) GC percentage = 41.65% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 1,585,824 number of insertions = 18,326 mapped reads with insertion percentage = 0.4% number of deletions = 74,261 mapped reads with deletion percentage = 1.62% homopolymer indels = 44.27% >>>>>>> Coverage mean coverageData = 0.0938X std coverageData = 0.9339X There is a 6.73% of reference with a coverageData >= 1X There is a 1.71% of reference with a coverageData >= 2X There is a 0.49% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% 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 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 30247743 0.1213547347591162 1.9746661940645271 chr2 243199373 22159996 0.09111863952050567 1.566849939018613 chr3 198022430 18508487 0.09346661890776717 0.40347574223147553 chr4 191154276 17766107 0.0929411958328361 0.43748534376439147 chr5 180915260 12704874 0.07022555200705567 0.3554043408542531 chr6 171115067 17295338 0.10107431392935141 0.6104079598586185 chr7 159138663 27541494 0.17306601350546724 1.3221973876099726 chr8 146364022 11293804 0.07716243271860895 0.9022721548527799 chr9 141213431 11951165 0.08463192853093414 0.6627411165986065 chr10 135534747 14759639 0.10889929945418352 0.6706812780531402 chr11 135006516 9278868 0.0687290382339768 0.46567152724104205 chr12 133851895 10594401 0.07915017564749458 0.40727765961672424 chr13 115169878 7903088 0.06862113720394841 0.38930698453484314 chr14 107349540 8983920 0.0836884815715093 0.4222971163433252 chr15 102531392 5431906 0.05297797966109735 0.3480959123233933 chr16 90354753 6200540 0.06862439212245978 0.4048177529367623 chr17 81195210 9730525 0.11984112116958623 0.5019699133711942 chr18 78077248 7874299 0.10085267093430342 1.2732947999773405 chr19 59128983 5322111 0.09000849887778384 1.2770171342336287 chr20 63025520 4977457 0.07897526271897479 0.40835392253036484 chr21 48129895 5197141 0.10798155699280042 0.4666309555321233 chr22 51304566 2779482 0.054176113681577584 0.29719604918265474 chrMT 16571 259145 15.638464787882445 9.116004838766377 chrX 155270560 20461915 0.13178232241836443 0.5673466634737749 chrY 59373566 1009784 0.01700729917418132 0.46556494677053645