BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004034.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 = 2,483,115 number of mapped reads = 2,273,318 (91.55%) number of supplementary alignments = 21,245 (0.86%) number of secondary alignments = 0 number of mapped bases = 148,891,535 bp number of sequenced bases = 148,825,366 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 68,466 duplication rate = 1.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.2051 >>>>>>> ACTG content number of A's = 40,328,276 bp (27.1%) number of C's = 29,046,419 bp (19.52%) number of T's = 44,389,057 bp (29.83%) number of G's = 35,042,030 bp (23.55%) number of N's = 19,584 bp (0.01%) GC percentage = 43.06% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,224,537 number of insertions = 12,005 mapped reads with insertion percentage = 0.52% number of deletions = 39,912 mapped reads with deletion percentage = 1.73% homopolymer indels = 44.66% >>>>>>> Coverage mean coverageData = 0.0481X std coverageData = 0.4497X There is a 4.23% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.06% 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 14203360 0.05698425120473421 0.8871791736930805 chr2 243199373 14812418 0.06090648103767932 0.5618025406591259 chr3 198022430 8269492 0.04176038037711183 0.23191543068978082 chr4 191154276 8232129 0.04306536674073668 0.2506570930069207 chr5 180915260 3672018 0.02029689480036123 0.16688355916906936 chr6 171115067 9142838 0.053430934869107695 0.287261313022944 chr7 159138663 9063356 0.056952570978933005 0.6279208657056493 chr8 146364022 9253974 0.06322574273068282 0.36521994955696835 chr9 141213431 7631327 0.0540410848030454 0.45278114080664295 chr10 135534747 6670301 0.049214693262385326 0.45161071782675777 chr11 135006516 7253773 0.05372905852929351 0.38935653753438354 chr12 133851895 3667750 0.027401554531596282 0.19769906058667913 chr13 115169878 2285939 0.019848410362994392 0.1534931856843955 chr14 107349540 4804310 0.04475389461380086 0.3046597305855938 chr15 102531392 5638168 0.05498967574730674 0.2643751407347214 chr16 90354753 4446777 0.04921464397119209 0.3166023054359667 chr17 81195210 5446060 0.0670736611186793 0.3181628956510196 chr18 78077248 3892789 0.049858173792191034 0.8793373815608307 chr19 59128983 3600462 0.060891661201072915 0.6000236028544373 chr20 63025520 2617346 0.04152835232458217 0.2354809471673866 chr21 48129895 1925718 0.040010849805510694 0.26575707644055796 chr22 51304566 1826619 0.03560343927283197 0.20610242183833635 chrMT 16571 16855 1.0171383742683 1.245576805331458 chrX 155270560 10087547 0.06496754439476485 0.3302466018151669 chrY 59373566 430209 0.007245800260674927 0.15305720705003045