BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068934.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 = 1,653,976 number of mapped reads = 1,053,562 (63.7%) number of supplementary alignments = 7,371 (0.45%) number of secondary alignments = 0 number of mapped bases = 65,568,462 bp number of sequenced bases = 65,535,220 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 166,153 duplication rate = 12.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7984 >>>>>>> ACTG content number of A's = 17,252,024 bp (26.32%) number of C's = 12,441,296 bp (18.98%) number of T's = 20,460,774 bp (31.22%) number of G's = 15,369,048 bp (23.45%) number of N's = 12,078 bp (0.02%) GC percentage = 42.44% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 676,072 number of insertions = 5,097 mapped reads with insertion percentage = 0.48% number of deletions = 21,292 mapped reads with deletion percentage = 2% homopolymer indels = 46.96% >>>>>>> Coverage mean coverageData = 0.0212X std coverageData = 0.2815X There is a 1.13% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.12% 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 0.02% 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 6226875 0.02498238509905257 0.3579562676644449 chr2 243199373 5554663 0.022839956088209157 0.2950968621506633 chr3 198022430 4049336 0.02044887541274996 0.24284917591133579 chr4 191154276 4194024 0.021940518871782916 0.2508434077833196 chr5 180915260 4320479 0.02388123036166214 0.26346529321438855 chr6 171115067 3690171 0.021565435847913966 0.27449464771804133 chr7 159138663 3807669 0.02392673740133157 0.30497104547022 chr8 146364022 3462759 0.02365853952824554 0.2738576227880304 chr9 141213431 2576294 0.01824397284136521 0.2404526596611764 chr10 135534747 3109873 0.022945208286698614 0.4321664654073844 chr11 135006516 3106735 0.02301174115181226 0.27665946106308076 chr12 133851895 2896586 0.021640231540987896 0.24855457537981113 chr13 115169878 1717624 0.014913830159653377 0.21014373786451582 chr14 107349540 1759187 0.01638746658811952 0.22862284391982948 chr15 102531392 1983536 0.019345645868145436 0.24116811795025062 chr16 90354753 1750546 0.019374144047519005 0.2400204776141212 chr17 81195210 1724684 0.02124120376066519 0.25047422196257707 chr18 78077248 1317659 0.016876350457434155 0.28220183675005434 chr19 59128983 1198420 0.020267894680346524 0.2927596324911802 chr20 63025520 1501472 0.023823238586528125 0.268347027630648 chr21 48129895 861169 0.017892600846106145 0.23193374963084715 chr22 51304566 740307 0.014429651349160619 0.20125233653258062 chrMT 16571 277955 16.77358035121598 11.652877742525904 chrX 155270560 3564755 0.02295834445370713 0.25740520885149853 chrY 59373566 175684 0.0029589598846058865 0.08793623393396295