BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231869.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 = 4,384,227 number of mapped reads = 4,040,408 (92.16%) number of supplementary alignments = 22,853 (0.52%) number of secondary alignments = 0 number of mapped bases = 271,337,410 bp number of sequenced bases = 271,230,169 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 315,043 duplication rate = 6.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9944 >>>>>>> ACTG content number of A's = 74,782,186 bp (27.57%) number of C's = 49,736,947 bp (18.34%) number of T's = 86,896,924 bp (32.04%) number of G's = 59,703,820 bp (22.01%) number of N's = 110,292 bp (0.04%) GC percentage = 40.35% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 1,642,067 number of insertions = 18,166 mapped reads with insertion percentage = 0.45% number of deletions = 60,607 mapped reads with deletion percentage = 1.48% homopolymer indels = 45.73% >>>>>>> Coverage mean coverageData = 0.0876X std coverageData = 0.7809X There is a 6.72% of reference with a coverageData >= 1X There is a 1.41% of reference with a coverageData >= 2X There is a 0.33% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 28976394 0.11625404937306054 1.3875551565589876 chr2 243199373 18510289 0.0761115819159616 0.8662178408118417 chr3 198022430 31551593 0.159333430056383 0.5010884387434398 chr4 191154276 11800869 0.06173478954768451 0.34220342857219593 chr5 180915260 21849670 0.12077295193340794 0.43446442473970825 chr6 171115067 13368520 0.07812590810603487 0.40908291883687037 chr7 159138663 18221192 0.11449883803535536 1.1977006695427126 chr8 146364022 22182818 0.15155922676134168 1.4946385173487007 chr9 141213431 10349699 0.07329118007195788 0.6597019060258257 chr10 135534747 13953990 0.1029550746864935 0.5482333018307698 chr11 135006516 8486980 0.06286348430767594 0.5186514555814944 chr12 133851895 2122974 0.015860619679684027 0.2133498594564623 chr13 115169878 14697581 0.12761653702541909 0.4534965732836304 chr14 107349540 12294750 0.1145300669197092 0.5036288626517813 chr15 102531392 4819918 0.04700919304792039 0.30941422453100287 chr16 90354753 6786670 0.07511137792607324 0.4582815516609846 chr17 81195210 6376526 0.07853327800987275 0.39047687164397266 chr18 78077248 4305949 0.055149856203948175 1.6349645801445551 chr19 59128983 3489017 0.059006883307970985 0.857820631013229 chr20 63025520 7098618 0.11263085175655829 0.4631858265326586 chr21 48129895 2271699 0.04719933421836885 0.29968880724940894 chr22 51304566 2449785 0.04774984355193649 0.26143195081893666 chrMT 16571 163640 9.875082976283869 6.296662991051759 chrX 155270560 4741632 0.03053786886580431 0.32485736237632507 chrY 59373566 466637 0.007859339289137526 0.15166686817504788