BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238306.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 = 2,217,267 number of mapped reads = 2,041,919 (92.09%) number of supplementary alignments = 22,340 (1.01%) number of secondary alignments = 0 number of mapped bases = 136,047,028 bp number of sequenced bases = 135,986,245 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 87,999 duplication rate = 3.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9391 >>>>>>> ACTG content number of A's = 38,419,579 bp (28.25%) number of C's = 25,258,865 bp (18.57%) number of T's = 42,883,380 bp (31.54%) number of G's = 29,381,077 bp (21.61%) number of N's = 43,344 bp (0.03%) GC percentage = 40.18% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,117,669 number of insertions = 10,480 mapped reads with insertion percentage = 0.51% number of deletions = 34,686 mapped reads with deletion percentage = 1.68% homopolymer indels = 47.1% >>>>>>> Coverage mean coverageData = 0.0439X std coverageData = 0.3985X There is a 3.67% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% 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 14641300 0.058741277920426924 0.602963603762655 chr2 243199373 11628470 0.047814555837691244 0.44287640781777193 chr3 198022430 6961877 0.03515701226371174 0.21686745563163085 chr4 191154276 10246780 0.05360476477125733 0.29855653661293546 chr5 180915260 6656104 0.03679128007222829 0.22585631874424245 chr6 171115067 8758448 0.05118455173792499 0.3027242493762228 chr7 159138663 9462397 0.059460076021877854 0.543726491516368 chr8 146364022 4812855 0.03288277360948717 0.7656487702214186 chr9 141213431 8682613 0.061485744935975674 0.4267277187509808 chr10 135534747 5731236 0.042286100995193504 0.4266514210595971 chr11 135006516 1995555 0.014781175450820463 0.19450229744281117 chr12 133851895 10853682 0.08108724945582578 0.33831208801931134 chr13 115169878 4321918 0.03752646156315283 0.2230035299884039 chr14 107349540 3347754 0.0311855458346631 0.25617635715646075 chr15 102531392 2964269 0.02891084322740883 0.2010387965155599 chr16 90354753 3587434 0.03970387700578408 0.2600541579690067 chr17 81195210 2317429 0.028541449674186446 0.20369370397041042 chr18 78077248 5213843 0.06677800682728982 0.6976789715069143 chr19 59128983 1299581 0.02197874771497423 0.44670955837169746 chr20 63025520 2888220 0.045826198657305806 0.25276057671224933 chr21 48129895 1098081 0.0228149469264373 0.2138313773848552 chr22 51304566 2108763 0.04110283283558037 0.23385926366540497 chrMT 16571 11105 0.6701466417234928 1.1304595300248785 chrX 155270560 6170244 0.039738660052491596 0.2651819195530354 chrY 59373566 287070 0.004834979930294232 0.15471379675432254