BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082795.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,598,100 number of mapped reads = 3,147,425 (87.47%) number of supplementary alignments = 23,698 (0.66%) number of secondary alignments = 0 number of mapped bases = 215,514,125 bp number of sequenced bases = 215,435,103 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 165,462 duplication rate = 4.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5732 >>>>>>> ACTG content number of A's = 61,934,007 bp (28.75%) number of C's = 39,013,914 bp (18.11%) number of T's = 70,141,874 bp (32.56%) number of G's = 44,333,226 bp (20.58%) number of N's = 12,082 bp (0.01%) GC percentage = 38.69% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,876,667 number of insertions = 17,188 mapped reads with insertion percentage = 0.54% number of deletions = 46,031 mapped reads with deletion percentage = 1.45% homopolymer indels = 47.76% >>>>>>> Coverage mean coverageData = 0.0696X std coverageData = 0.5189X There is a 5.32% of reference with a coverageData >= 1X There is a 1.14% of reference with a coverageData >= 2X There is a 0.28% of reference with a coverageData >= 3X There is a 0.08% 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 20476791 0.08215342019147868 1.0181578326913063 chr2 243199373 19129624 0.07865819621171474 0.5502416532867986 chr3 198022430 18013376 0.09096634154019825 0.3742764642601477 chr4 191154276 10948715 0.057276851081270085 0.3031398087325808 chr5 180915260 13898206 0.07682163461501258 0.3472846879268887 chr6 171115067 15802285 0.09234888123557232 0.5724692082551617 chr7 159138663 11251469 0.07070229690191629 0.48762275688720313 chr8 146364022 19415219 0.13265021509179353 0.7550666644651838 chr9 141213431 6380879 0.04518606307356132 0.4260450963213145 chr10 135534747 8708472 0.06425268938599192 0.43896366069266884 chr11 135006516 8625223 0.06388745710614442 0.4089382599773973 chr12 133851895 7532544 0.0562752137353005 0.2978965669609229 chr13 115169878 5243914 0.04553199231486552 0.2629099608141352 chr14 107349540 4757895 0.04432152201117955 0.2834928487829056 chr15 102531392 3975219 0.038770750327860565 0.2415456255195683 chr16 90354753 7137282 0.07899177146773895 0.4140965502177945 chr17 81195210 4818418 0.05934362384184978 0.36823879722783387 chr18 78077248 6034720 0.07729165864042749 0.8874435727741646 chr19 59128983 3237766 0.054757681186568014 0.6297382610224295 chr20 63025520 4684491 0.07432689170989783 0.3471701917102338 chr21 48129895 3520260 0.07314082027396902 0.34238660600144927 chr22 51304566 2379173 0.04637351381161669 0.2611336000035632 chrMT 16571 62149 3.7504676845090823 2.9841746596698635 chrX 155270560 9134481 0.058829445839571906 0.3333038334037942 chrY 59373566 345554 0.005819997404232045 0.11877066866094764