BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230352.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 = 2,242,934 number of mapped reads = 1,836,907 (81.9%) number of supplementary alignments = 9,981 (0.44%) number of secondary alignments = 0 number of mapped bases = 120,160,594 bp number of sequenced bases = 120,108,054 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 81,353 duplication rate = 3.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1715 >>>>>>> ACTG content number of A's = 32,500,615 bp (27.06%) number of C's = 20,600,741 bp (17.15%) number of T's = 40,146,891 bp (33.43%) number of G's = 26,634,758 bp (22.18%) number of N's = 225,049 bp (0.19%) GC percentage = 39.33% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 1,117,585 number of insertions = 10,453 mapped reads with insertion percentage = 0.56% number of deletions = 32,275 mapped reads with deletion percentage = 1.74% homopolymer indels = 48.08% >>>>>>> Coverage mean coverageData = 0.0388X std coverageData = 0.3519X There is a 3.33% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 10948110 0.043924103202134045 0.61087761821371 chr2 243199373 10645268 0.043771774033315454 0.35817335223536606 chr3 198022430 5173431 0.026125479825694492 0.18206394864920072 chr4 191154276 8348210 0.04367263016392058 0.2470168143830854 chr5 180915260 7851455 0.04339852260113381 0.23500637642577982 chr6 171115067 5964184 0.034854814976637914 0.2746153779536688 chr7 159138663 6271170 0.0394069541730409 0.48963473294048016 chr8 146364022 6264376 0.04279997170342859 0.5424541118170589 chr9 141213431 4943624 0.035008171425280364 0.35556565584209415 chr10 135534747 5315874 0.03922148465736244 0.31215607184044025 chr11 135006516 6292405 0.04660815778699155 0.3443540367993706 chr12 133851895 5085435 0.03799299965084544 0.2243733062169023 chr13 115169878 4303702 0.03736829520649488 0.2174595637091807 chr14 107349540 4498173 0.041902117139952344 0.24465855362407318 chr15 102531392 3527397 0.03440309285959953 0.20932079362731823 chr16 90354753 3270679 0.0361981953511621 0.24389905744151627 chr17 81195210 3273976 0.04032228009509428 0.2519765543583864 chr18 78077248 3572790 0.04575968148877378 0.5863165235351758 chr19 59128983 1777455 0.030060638790286653 0.40074993608742504 chr20 63025520 2762695 0.04383454511759681 0.24498002613200187 chr21 48129895 1558996 0.032391427407020106 0.22136780866777422 chr22 51304566 1252623 0.024415429223200134 0.17439927784003345 chrMT 16571 42744 2.5794460201556935 2.1374864249737446 chrX 155270560 6933516 0.04465441484850702 0.26674383351497827 chrY 59373566 282306 0.004754742202952742 0.11195394413585356