BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240212.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 = 2,427,655 number of mapped reads = 2,034,382 (83.8%) number of supplementary alignments = 16,974 (0.7%) number of secondary alignments = 0 number of mapped bases = 135,501,803 bp number of sequenced bases = 135,446,053 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 147,847 duplication rate = 5.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.76 >>>>>>> ACTG content number of A's = 38,118,821 bp (28.14%) number of C's = 25,133,315 bp (18.56%) number of T's = 42,998,514 bp (31.75%) number of G's = 29,182,189 bp (21.55%) number of N's = 13,214 bp (0.01%) GC percentage = 40.1% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,075,098 number of insertions = 10,636 mapped reads with insertion percentage = 0.52% number of deletions = 31,139 mapped reads with deletion percentage = 1.51% homopolymer indels = 47.82% >>>>>>> Coverage mean coverageData = 0.0438X std coverageData = 0.4207X There is a 2.99% of reference with a coverageData >= 1X There is a 0.87% of reference with a coverageData >= 2X There is a 0.28% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% 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 10543725 0.04230170002264508 0.6182721648775689 chr2 243199373 11215736 0.04611745442287797 0.4706414778907857 chr3 198022430 9178114 0.0463488605810968 0.2997662414650285 chr4 191154276 9473145 0.04955758876144628 0.33337340576870444 chr5 180915260 9833760 0.05435561378293904 0.3246284717266909 chr6 171115067 7935258 0.04637381230724703 0.338251431777109 chr7 159138663 8910027 0.05598907790245793 0.5421073154847653 chr8 146364022 7710293 0.052678881699493064 0.692392765197977 chr9 141213431 6040572 0.04277618606972307 0.41044159468541336 chr10 135534747 4654891 0.034344631934126825 0.3529627915488203 chr11 135006516 6046693 0.044788156743486365 0.3779562181092245 chr12 133851895 4673897 0.03491842233537299 0.261570500868482 chr13 115169878 4483589 0.0389302227097957 0.274584466514377 chr14 107349540 4970664 0.04630354261415559 0.317493143063852 chr15 102531392 3805323 0.03711373585955022 0.26997352741119995 chr16 90354753 3172438 0.03511091441974281 0.28464811540523344 chr17 81195210 2838135 0.034954463446796924 0.27451525658837367 chr18 78077248 3843885 0.04923181974856491 0.8226973159472593 chr19 59128983 2632240 0.04451691651791136 0.43473978406526886 chr20 63025520 3536023 0.05610462238153688 0.3369332043911602 chr21 48129895 2011929 0.04180206501593241 0.30534895993801126 chr22 51304566 1602213 0.031229442619200794 0.2363587274174222 chrMT 16571 16217 0.9786373785528936 1.5736751284651653 chrX 155270560 5979519 0.03851032030798369 0.30060158380027985 chrY 59373566 393517 0.006627814809034714 0.17335891636627881