BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237286.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 = 2,591,722 number of mapped reads = 2,106,423 (81.28%) number of supplementary alignments = 23,508 (0.91%) number of secondary alignments = 0 number of mapped bases = 128,348,145 bp number of sequenced bases = 128,262,365 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 800,549 duplication rate = 22.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7997 >>>>>>> ACTG content number of A's = 32,240,066 bp (25.14%) number of C's = 22,198,780 bp (17.31%) number of T's = 42,912,463 bp (33.46%) number of G's = 30,898,410 bp (24.09%) number of N's = 12,646 bp (0.01%) GC percentage = 41.4% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 892,916 number of insertions = 10,876 mapped reads with insertion percentage = 0.51% number of deletions = 49,559 mapped reads with deletion percentage = 2.32% homopolymer indels = 40.92% >>>>>>> Coverage mean coverageData = 0.0415X std coverageData = 0.756X There is a 1.34% of reference with a coverageData >= 1X There is a 0.78% of reference with a coverageData >= 2X There is a 0.55% of reference with a coverageData >= 3X There is a 0.4% of reference with a coverageData >= 4X There is a 0.29% of reference with a coverageData >= 5X There is a 0.2% of reference with a coverageData >= 6X There is a 0.14% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% 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 9779287 0.03923475480528492 0.6681041978312698 chr2 243199373 10434488 0.042905077719916654 1.6798022165425484 chr3 198022430 10002577 0.05051234347543357 0.5384648743507419 chr4 191154276 7793800 0.04077230268184009 0.6601705428921981 chr5 180915260 7443539 0.041143787428434726 0.48154076505633636 chr6 171115067 15078436 0.08811869266895124 0.8478010808939797 chr7 159138663 5868605 0.036877304919923824 0.5990693083444706 chr8 146364022 6644215 0.04539513815765462 0.9501186235931929 chr9 141213431 4948185 0.035040470052738824 0.4604120565312452 chr10 135534747 4635538 0.034201841982263045 0.8009254853087778 chr11 135006516 4905740 0.036337060946006486 0.4908271435991249 chr12 133851895 3670013 0.027418461277668126 0.3931904438651033 chr13 115169878 3519888 0.030562574703778014 0.478614472410998 chr14 107349540 3958579 0.036875602820468534 0.4565740706837675 chr15 102531392 2691371 0.026249238867253454 0.40701756964156727 chr16 90354753 3329733 0.036851774693025835 0.48117019531003397 chr17 81195210 3908742 0.04814005653781793 0.5452037036290238 chr18 78077248 3536533 0.04529530805184117 0.9922617057663403 chr19 59128983 1972775 0.03336392577562174 0.5751862933840326 chr20 63025520 1426294 0.022630420185347142 0.3718334803648847 chr21 48129895 2129802 0.044251125002454296 0.5794602271036908 chr22 51304566 1814432 0.03536589706265131 0.4534521091993518 chrMT 16571 5609 0.3384828917989258 0.8698451847575318 chrX 155270560 8372760 0.053923680058859835 0.5744380003669386 chrY 59373566 477204 0.008037314113826344 0.4531120138248534