BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237598.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 = 862,629 number of mapped reads = 665,483 (77.15%) number of supplementary alignments = 2,817 (0.33%) number of secondary alignments = 0 number of mapped bases = 41,323,869 bp number of sequenced bases = 41,296,320 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 58,613 duplication rate = 7.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6033 >>>>>>> ACTG content number of A's = 11,022,561 bp (26.69%) number of C's = 6,901,886 bp (16.71%) number of T's = 13,846,985 bp (33.53%) number of G's = 9,446,904 bp (22.88%) number of N's = 77,984 bp (0.19%) GC percentage = 39.59% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 431,505 number of insertions = 3,437 mapped reads with insertion percentage = 0.51% number of deletions = 17,380 mapped reads with deletion percentage = 2.57% homopolymer indels = 49.94% >>>>>>> Coverage mean coverageData = 0.0133X std coverageData = 0.1614X There is a 1.01% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.06% 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 3470096 0.013922115764758717 0.18268579177516742 chr2 243199373 3702020 0.015222160955160028 0.1805337451189812 chr3 198022430 3022387 0.015262851789062481 0.1617639029136459 chr4 191154276 2756893 0.01442234543578821 0.15633849418298085 chr5 180915260 2463866 0.013618895387818583 0.14882523203453665 chr6 171115067 2314841 0.013527978807383455 0.1543138945195592 chr7 159138663 2405190 0.01511380047223345 0.19556049201182865 chr8 146364022 2217621 0.01515140790542091 0.18731618612704407 chr9 141213431 1688362 0.011956100691300391 0.1549032907452762 chr10 135534747 1898027 0.014003988217132246 0.16671922559746347 chr11 135006516 1827119 0.0135335615949085 0.1580349429225971 chr12 133851895 2196145 0.016407276116636227 0.1663361294240381 chr13 115169878 1465755 0.012726895482167655 0.14656369217796197 chr14 107349540 1208703 0.01125950795876722 0.13882222812711872 chr15 102531392 1139636 0.011114995883407103 0.13629000747144587 chr16 90354753 934359 0.010341005525188032 0.13214212833491773 chr17 81195210 829584 0.010217154435588011 0.1330052989339172 chr18 78077248 1099176 0.01407805766924572 0.2091167153313849 chr19 59128983 545602 0.009227319198099517 0.1388051957225234 chr20 63025520 756442 0.012002154048074495 0.1406810282835213 chr21 48129895 529245 0.01099618023268075 0.13907556348555392 chr22 51304566 349031 0.006803117679623291 0.10276336111497313 chrMT 16571 24905 1.50292679983103 1.700611397257734 chrX 155270560 2362428 0.015214912601590412 0.16014891808828163 chrY 59373566 116436 0.0019610747314722514 0.056460148739565154