BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472806.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 2,947,015 number of mapped reads = 2,278,816 (77.33%) number of supplementary alignments = 17,086 (0.58%) number of secondary alignments = 0 number of mapped bases = 142,552,382 bp number of sequenced bases = 142,482,719 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 191,805 duplication rate = 5.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1045 >>>>>>> ACTG content number of A's = 38,377,171 bp (26.93%) number of C's = 27,452,293 bp (19.27%) number of T's = 42,895,578 bp (30.11%) number of G's = 33,754,413 bp (23.69%) number of N's = 3,264 bp (0%) GC percentage = 42.96% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,263,445 number of insertions = 10,732 mapped reads with insertion percentage = 0.47% number of deletions = 38,784 mapped reads with deletion percentage = 1.68% homopolymer indels = 46.55% >>>>>>> Coverage mean coverageData = 0.046X std coverageData = 0.3839X There is a 3.3% of reference with a coverageData >= 1X There is a 0.7% of reference with a coverageData >= 2X There is a 0.25% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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 11078529 0.04444734763569556 0.4356834740574893 chr2 243199373 11947210 0.04912516776924421 0.49621456219791604 chr3 198022430 11328441 0.057207867815782285 0.3328117229724937 chr4 191154276 7659615 0.04007033041730126 0.3027953108523685 chr5 180915260 7554996 0.041759860389886404 0.29948218831945517 chr6 171115067 8688779 0.05077740465718311 0.35915214755510094 chr7 159138663 9021387 0.0566888449980254 0.5507391427146355 chr8 146364022 6999795 0.0478245603280839 0.3886027960221514 chr9 141213431 5806029 0.04111527465117677 0.39025572573319545 chr10 135534747 6779276 0.05001873062115946 0.3711998099007716 chr11 135006516 5459728 0.040440477702572517 0.384032736925817 chr12 133851895 7269585 0.054310661795262595 0.3416346451822483 chr13 115169878 5669606 0.04922820183937331 0.32203532361876797 chr14 107349540 4118190 0.038362437323904694 0.3218304234113337 chr15 102531392 4143756 0.040414510318947 0.3242012760067279 chr16 90354753 4002821 0.04430116697900773 0.3178727528675225 chr17 81195210 3408261 0.04197613381380503 0.3206316868659886 chr18 78077248 3325399 0.042591139995098184 0.5732052640797782 chr19 59128983 2710221 0.04583574522159463 0.379807450832734 chr20 63025520 3880862 0.061576040943414664 0.36816162043602585 chr21 48129895 1891470 0.03929927542954332 0.3086111594431164 chr22 51304566 2117766 0.041278314292727866 0.28720075258259586 chrMT 16571 189505 11.435942308852816 8.447541399482208 chrX 155270560 7007836 0.04513306321558962 0.33715986000719866 chrY 59373566 493319 0.008308731195293205 0.1412862204102256