BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080637.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 = 2,685,483 number of mapped reads = 2,303,359 (85.77%) number of supplementary alignments = 15,540 (0.58%) number of secondary alignments = 0 number of mapped bases = 153,181,022 bp number of sequenced bases = 153,121,383 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 94,315 duplication rate = 3.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4531 >>>>>>> ACTG content number of A's = 41,716,031 bp (27.24%) number of C's = 27,471,215 bp (17.94%) number of T's = 49,028,270 bp (32.02%) number of G's = 34,782,010 bp (22.72%) number of N's = 123,857 bp (0.08%) GC percentage = 40.66% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 1,388,100 number of insertions = 13,439 mapped reads with insertion percentage = 0.58% number of deletions = 36,545 mapped reads with deletion percentage = 1.57% homopolymer indels = 47.13% >>>>>>> Coverage mean coverageData = 0.0495X std coverageData = 0.4493X There is a 4.22% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 18025531 0.07231890106303887 0.5855035114962927 chr2 243199373 10590615 0.04354704894736715 0.47024749181722414 chr3 198022430 9432707 0.0476345381682267 0.2457225190080158 chr4 191154276 6598243 0.034517893808454485 0.22129239224068026 chr5 180915260 7032880 0.03887389046120267 0.22061539366899363 chr6 171115067 9457650 0.055270702725435626 0.41717500214557207 chr7 159138663 9923772 0.06235927720468532 1.2214532091234354 chr8 146364022 17773333 0.12143238998993892 0.554085922799246 chr9 141213431 4838134 0.0342611461653389 0.3594982370028038 chr10 135534747 7435398 0.05485971800279378 0.3804458609520698 chr11 135006516 6323730 0.046840183624914815 0.32070286647151286 chr12 133851895 4866153 0.036354756128032406 0.2163642338360246 chr13 115169878 3197096 0.02775982796473918 0.1840013110461527 chr14 107349540 3030170 0.02822713539340737 0.21738240761688687 chr15 102531392 2742990 0.026752684680219692 0.18316811229944174 chr16 90354753 3831696 0.04240724336881315 0.25225982199129204 chr17 81195210 2545665 0.031352403670117976 0.22415821623990465 chr18 78077248 4860762 0.06225580594234059 0.5471492999071664 chr19 59128983 2598011 0.043938029510840734 0.4235265743304854 chr20 63025520 4078338 0.06470931140274606 0.2942060443336071 chr21 48129895 2227158 0.046273901075412696 0.2576515774951758 chr22 51304566 1493298 0.02910653215544207 0.18937767081450893 chrMT 16571 47915 2.8914971938929455 3.3475194250786933 chrX 155270560 9885407 0.0636656878161578 0.3215287613207923 chrY 59373566 344370 0.005800055869980927 0.12169256785604539