BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008748.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 = 985,258 number of mapped reads = 714,401 (72.51%) number of supplementary alignments = 5,593 (0.57%) number of secondary alignments = 0 number of mapped bases = 45,613,951 bp number of sequenced bases = 45,585,438 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,712 duplication rate = 2.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9275 >>>>>>> ACTG content number of A's = 13,430,469 bp (29.46%) number of C's = 7,904,675 bp (17.34%) number of T's = 13,797,709 bp (30.27%) number of G's = 10,445,520 bp (22.91%) number of N's = 7,065 bp (0.02%) GC percentage = 40.25% >>>>>>> Mismatches and indels general error rate = 0.0109 number of mismatches = 490,609 number of insertions = 3,788 mapped reads with insertion percentage = 0.53% number of deletions = 18,459 mapped reads with deletion percentage = 2.55% homopolymer indels = 48.69% >>>>>>> Coverage mean coverageData = 0.0147X std coverageData = 0.157X There is a 1.28% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% 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 3634344 0.01458108302967879 0.18328917171354125 chr2 243199373 4075459 0.016757687117885785 0.1841437766672521 chr3 198022430 3554737 0.017951183610866707 0.15304407805009276 chr4 191154276 2593420 0.013567156614377802 0.1339546954437549 chr5 180915260 2472776 0.013668144964664673 0.1337480145021323 chr6 171115067 2511835 0.014679215828492765 0.1460918849022882 chr7 159138663 2659359 0.016710954772819725 0.19659260565496398 chr8 146364022 3445442 0.023540224933146482 0.21307350507758738 chr9 141213431 1576544 0.01116426382983358 0.14534838232705846 chr10 135534747 2382286 0.017576939144616548 0.16407047107633807 chr11 135006516 2046994 0.0151621866903076 0.16390645831098605 chr12 133851895 2098039 0.015674331693249468 0.1435224376185925 chr13 115169878 1373603 0.011926755709509391 0.125301608237155 chr14 107349540 1586857 0.01478214997474605 0.14025001581849697 chr15 102531392 1263486 0.012322918623790848 0.12590063242654653 chr16 90354753 1140759 0.012625334718141501 0.13185174302160196 chr17 81195210 1149026 0.014151401295716829 0.14388618881949086 chr18 78077248 899388 0.011519207234353342 0.19260267189837388 chr19 59128983 762318 0.012892459185371073 0.14472390353170167 chr20 63025520 1001920 0.01589705249556053 0.14448254625868887 chr21 48129895 506841 0.010530689917358017 0.12229619533062697 chr22 51304566 490423 0.00955905172260886 0.10930613672175837 chrMT 16571 18183 1.0972783778890833 1.573656820130471 chrX 155270560 2268178 0.014607907641989569 0.1412940024690801 chrY 59373566 101734 0.0017134561195128485 0.050650446510353685