BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013319.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 = 1,903,496 number of mapped reads = 1,658,798 (87.14%) number of supplementary alignments = 19,599 (1.03%) number of secondary alignments = 0 number of mapped bases = 107,170,197 bp number of sequenced bases = 107,103,810 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 175,507 duplication rate = 8.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8783 >>>>>>> ACTG content number of A's = 29,366,235 bp (27.42%) number of C's = 19,253,593 bp (17.98%) number of T's = 34,575,614 bp (32.28%) number of G's = 23,896,021 bp (22.31%) number of N's = 12,347 bp (0.01%) GC percentage = 40.29% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 851,176 number of insertions = 6,960 mapped reads with insertion percentage = 0.42% number of deletions = 38,152 mapped reads with deletion percentage = 2.27% homopolymer indels = 44.05% >>>>>>> Coverage mean coverageData = 0.0346X std coverageData = 0.3895X There is a 2.24% of reference with a coverageData >= 1X There is a 0.74% of reference with a coverageData >= 2X There is a 0.26% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% 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 7474392 0.029987455878795984 0.7851879028924721 chr2 243199373 6042997 0.024847913567606114 0.38591087450998296 chr3 198022430 7705393 0.03891171823313147 0.2815226172105835 chr4 191154276 7173112 0.03752525002370337 0.27894560365405763 chr5 180915260 10775473 0.05956088502429259 0.3535311442849082 chr6 171115067 4322776 0.0252623925863875 0.2868785120985814 chr7 159138663 6268192 0.03938824093300319 0.4111408955158459 chr8 146364022 13155361 0.08988111163001519 0.5509061360915596 chr9 141213431 2203611 0.015604825861075495 0.27486558937641514 chr10 135534747 4582233 0.033808548002823215 0.36258425314773945 chr11 135006516 4403224 0.032614899861574086 0.32561265696040953 chr12 133851895 4969816 0.03712921658673566 0.2772742098762471 chr13 115169878 1587835 0.013786894868465521 0.16593507995933282 chr14 107349540 2540207 0.023662951885960574 0.22222545638515245 chr15 102531392 1632941 0.015926254078360704 0.17905761754435578 chr16 90354753 3719600 0.04116662241332229 0.29525466759935326 chr17 81195210 2355491 0.029010221169450758 0.2654152226234111 chr18 78077248 2689102 0.034441557161440935 0.48689152088661497 chr19 59128983 2545060 0.04304251267098573 0.5570682426320125 chr20 63025520 3345204 0.05307697580281765 0.3319643941710962 chr21 48129895 1655849 0.034403752594930864 0.2694866017273294 chr22 51304566 1028353 0.02004408340575379 0.19484583770910502 chrMT 16571 19450 1.1737372518254783 2.270772767134681 chrX 155270560 4759418 0.030652417303061185 0.2772972480748084 chrY 59373566 215107 0.0036229422366175546 0.09489236664817986