BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008728.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 = 2,375,099 number of mapped reads = 2,068,811 (87.1%) number of supplementary alignments = 18,132 (0.76%) number of secondary alignments = 0 number of mapped bases = 132,481,984 bp number of sequenced bases = 132,393,164 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 115,612 duplication rate = 4.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1918 >>>>>>> ACTG content number of A's = 34,777,915 bp (26.27%) number of C's = 24,322,867 bp (18.37%) number of T's = 41,977,446 bp (31.71%) number of G's = 31,219,776 bp (23.58%) number of N's = 95,160 bp (0.07%) GC percentage = 41.95% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 1,181,771 number of insertions = 10,071 mapped reads with insertion percentage = 0.48% number of deletions = 52,874 mapped reads with deletion percentage = 2.52% homopolymer indels = 44.15% >>>>>>> Coverage mean coverageData = 0.0428X std coverageData = 0.358X There is a 3.46% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% 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 12696490 0.050938649416644784 0.6489337488060782 chr2 243199373 12517399 0.05146970095190172 0.5059129719078359 chr3 198022430 9408424 0.04751191064567786 0.25955633341204926 chr4 191154276 6995783 0.03659757524859135 0.23887464203590775 chr5 180915260 5592697 0.030913351366822234 0.20865994177843222 chr6 171115067 6704453 0.03918096236376426 0.26665878445080393 chr7 159138663 7289118 0.045803564404710374 0.41570699595669075 chr8 146364022 10001464 0.0683328038088486 0.39620804026061346 chr9 141213431 4025006 0.02850299699891861 0.2765787496492089 chr10 135534747 8183954 0.06038270023848571 0.36648755879660144 chr11 135006516 6006452 0.04449008964870999 0.344972016499754 chr12 133851895 5848662 0.04369502575962783 0.2507428486833838 chr13 115169878 2844354 0.024697030589890874 0.18597694404573342 chr14 107349540 4325966 0.040297946316304664 0.24449508701891876 chr15 102531392 3436161 0.03351325806636859 0.22109367038594355 chr16 90354753 4135519 0.045769800289310734 0.28958778293556664 chr17 81195210 4073906 0.0501742159420488 0.30971840528895844 chr18 78077248 2067107 0.026475151890599423 0.4547646763482333 chr19 59128983 3149422 0.053263591562195484 0.42957029376941047 chr20 63025520 3441430 0.054603754161806205 0.284356721726761 chr21 48129895 1617219 0.03360113293411506 0.22887960103578073 chr22 51304566 1914020 0.03730701084188101 0.22639420123008422 chrMT 16571 121275 7.318508237281999 5.425163204040139 chrX 155270560 5717416 0.036822279767652025 0.2497619074187005 chrY 59373566 368287 0.0062028782303559125 0.17077109689386968