BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716621.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 548,354 number of mapped reads = 496,925 (90.62%) number of supplementary alignments = 1,910 (0.35%) number of secondary alignments = 0 number of mapped bases = 28,379,796 bp number of sequenced bases = 28,371,965 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,463 duplication rate = 1.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5335 >>>>>>> ACTG content number of A's = 6,693,198 bp (23.59%) number of C's = 5,533,480 bp (19.5%) number of T's = 8,853,878 bp (31.21%) number of G's = 7,290,801 bp (25.7%) number of N's = 608 bp (0%) GC percentage = 45.2% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 139,648 number of insertions = 1,491 mapped reads with insertion percentage = 0.3% number of deletions = 4,586 mapped reads with deletion percentage = 0.92% homopolymer indels = 43.52% >>>>>>> Coverage mean coverageData = 0.0092X std coverageData = 0.1068X There is a 0.88% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 3139518 0.012595828196552417 0.13751431231139982 chr2 243199373 2349123 0.009659247764590248 0.116727110261168 chr3 198022430 1824162 0.009211895844324303 0.09905943936385297 chr4 191154276 1763175 0.009223832377152788 0.10150606052322315 chr5 180915260 1423669 0.007869258789999252 0.09155622708290463 chr6 171115067 1474266 0.008615641076188807 0.09805357601184703 chr7 159138663 1176062 0.00739017142553221 0.09351672453967166 chr8 146364022 1751083 0.011963889595764183 0.11725655905691955 chr9 141213431 1037044 0.0073438057035807025 0.10303931175623345 chr10 135534747 1344848 0.009922533001813918 0.1164024037565167 chr11 135006516 1099641 0.008145095752267247 0.1009357686199522 chr12 133851895 1260087 0.009414039300676318 0.1003331235024763 chr13 115169878 867101 0.0075288870237407044 0.08878167303102115 chr14 107349540 473026 0.004406409193742237 0.07223629453679178 chr15 102531392 809802 0.007898088421544106 0.09150884994455917 chr16 90354753 844618 0.009347798228168473 0.10227442526358446 chr17 81195210 646383 0.007960851385198708 0.09232623585985791 chr18 78077248 677550 0.00867794418163919 0.14732343344293905 chr19 59128983 550187 0.009304861543111607 0.1118381963108116 chr20 63025520 1503160 0.023850021388161495 0.16131204976265534 chr21 48129895 369566 0.007678512492080026 0.09267607101102415 chr22 51304566 338742 0.006602570227375084 0.08353848643831772 chrMT 16571 1304 0.0786916903023354 0.28143783469198175 chrX 155270560 1575457 0.010146527455043635 0.1082176789165824 chrY 59373566 80222 0.0013511400005854458 0.045211951156629626