BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238506.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 = 2,362,997 number of mapped reads = 2,095,163 (88.67%) number of supplementary alignments = 17,717 (0.75%) number of secondary alignments = 0 number of mapped bases = 128,561,377 bp number of sequenced bases = 128,487,329 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 405,238 duplication rate = 15.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.2883 >>>>>>> ACTG content number of A's = 31,665,830 bp (24.65%) number of C's = 22,692,373 bp (17.66%) number of T's = 42,653,257 bp (33.2%) number of G's = 31,467,230 bp (24.49%) number of N's = 8,639 bp (0.01%) GC percentage = 42.15% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 782,619 number of insertions = 8,444 mapped reads with insertion percentage = 0.4% number of deletions = 42,283 mapped reads with deletion percentage = 1.99% homopolymer indels = 41.05% >>>>>>> Coverage mean coverageData = 0.0415X std coverageData = 0.5693X There is a 2.63% of reference with a coverageData >= 1X There is a 0.87% of reference with a coverageData >= 2X There is a 0.33% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% 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 0.01% 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 25067114 0.1005699159321252 1.124373086392039 chr2 243199373 11255300 0.04628013576334344 1.0048480115882572 chr3 198022430 4226132 0.021341683363849236 0.2145476990418472 chr4 191154276 3707526 0.019395464635067854 0.2596986514246097 chr5 180915260 4606790 0.02546380001333221 0.23994802798144874 chr6 171115067 6488112 0.03791666107345182 0.4253163514489822 chr7 159138663 4325279 0.02717930965651006 0.47493136664984553 chr8 146364022 9999491 0.0683193237201421 0.4782203938375131 chr9 141213431 10506651 0.07440263242382376 0.6242492640196284 chr10 135534747 3228662 0.0238216551213985 0.3920675078087064 chr11 135006516 5203412 0.03854193230199348 0.3083903766416853 chr12 133851895 1167411 0.008721662102729288 0.22647410893938744 chr13 115169878 4817619 0.04183054704633793 0.3358130298053894 chr14 107349540 1850993 0.017242672861010864 0.35661468277828307 chr15 102531392 9046263 0.08822920301325861 0.4654240627597796 chr16 90354753 2007393 0.022216794726891677 0.3420391639269117 chr17 81195210 1174553 0.014465791762839212 0.18107084845529112 chr18 78077248 10624872 0.13608153811978618 1.079566049171518 chr19 59128983 2226698 0.037658317241816924 0.7056822698332726 chr20 63025520 1291365 0.02048955724601717 0.23986137842389854 chr21 48129895 2246358 0.04667282153846378 0.3914198312402158 chr22 51304566 1119682 0.02182421736108244 0.2162717796062016 chrMT 16571 95951 5.790296300766399 4.555586611703481 chrX 155270560 1906395 0.012277890927938948 0.21749688224538927 chrY 59373566 371355 0.00625455105728364 0.3470788013389113