BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063600.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 = 2,050,177 number of mapped reads = 1,066,106 (52%) number of supplementary alignments = 11,570 (0.56%) number of secondary alignments = 0 number of mapped bases = 68,324,565 bp number of sequenced bases = 68,292,392 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 225,677 duplication rate = 14.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6323 >>>>>>> ACTG content number of A's = 18,725,767 bp (27.42%) number of C's = 12,256,366 bp (17.95%) number of T's = 22,107,659 bp (32.37%) number of G's = 15,200,913 bp (22.26%) number of N's = 1,687 bp (0%) GC percentage = 40.21% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 555,500 number of insertions = 5,690 mapped reads with insertion percentage = 0.53% number of deletions = 19,357 mapped reads with deletion percentage = 1.8% homopolymer indels = 46.87% >>>>>>> Coverage mean coverageData = 0.0221X std coverageData = 0.3821X There is a 0.78% of reference with a coverageData >= 1X There is a 0.44% of reference with a coverageData >= 2X There is a 0.3% of reference with a coverageData >= 3X There is a 0.2% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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% 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 6094828 0.02445260908697997 0.4360528865991187 chr2 243199373 5626917 0.023137053893638123 0.4292880124291718 chr3 198022430 4695708 0.02371301069277859 0.3537193493231333 chr4 191154276 4497786 0.023529612280292385 0.4757384750556793 chr5 180915260 4289356 0.023709199544582366 0.3585741480139385 chr6 171115067 4310810 0.025192463034245837 0.4036320651874675 chr7 159138663 3703252 0.023270598924159617 0.383537404865299 chr8 146364022 3406778 0.023276061654004015 0.38137842546703854 chr9 141213431 2762401 0.019561885724595135 0.3389652845952676 chr10 135534747 3119298 0.023014747649914454 0.3709863712751656 chr11 135006516 3438971 0.025472629780328528 0.39243943227747585 chr12 133851895 3113166 0.023258288573351913 0.36067063786435 chr13 115169878 2151338 0.01867969331355895 0.3359507379930759 chr14 107349540 2091903 0.019486837111737973 0.3598844357012414 chr15 102531392 2034856 0.0198461755010602 0.45741594847781675 chr16 90354753 1664186 0.018418355922017737 0.30058467095945984 chr17 81195210 1597401 0.01967358665615866 0.3349440457181576 chr18 78077248 1611734 0.020642812615526612 0.400979008860149 chr19 59128983 1121076 0.018959839035283255 0.32686924032480996 chr20 63025520 1423895 0.02259235623918692 0.35516815298135995 chr21 48129895 817971 0.016995071358456112 0.28806255440145806 chr22 51304566 742371 0.01446988168655398 0.2860809925894869 chrMT 16571 19463 1.174521754872971 2.114624867028999 chrX 155270560 3788385 0.02439860460347409 0.3675038328042916 chrY 59373566 200715 0.003380544803389441 0.13291591954848297