BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240245.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 = 1,937,523 number of mapped reads = 1,364,923 (70.45%) number of supplementary alignments = 6,551 (0.34%) number of secondary alignments = 0 number of mapped bases = 85,025,343 bp number of sequenced bases = 84,973,909 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 309,575 duplication rate = 13.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7814 >>>>>>> ACTG content number of A's = 23,069,598 bp (27.15%) number of C's = 14,634,079 bp (17.22%) number of T's = 27,347,986 bp (32.18%) number of G's = 19,915,214 bp (23.44%) number of N's = 7,032 bp (0.01%) GC percentage = 40.66% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 850,333 number of insertions = 6,036 mapped reads with insertion percentage = 0.44% number of deletions = 29,946 mapped reads with deletion percentage = 2.16% homopolymer indels = 47.93% >>>>>>> Coverage mean coverageData = 0.0275X std coverageData = 0.4619X There is a 1.08% of reference with a coverageData >= 1X There is a 0.45% of reference with a coverageData >= 2X There is a 0.29% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.12% of reference with a coverageData >= 6X There is a 0.09% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% 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 5715907 0.022932368140418796 0.523334084904753 chr2 243199373 6028780 0.024789455357683014 0.4464334220235965 chr3 198022430 4474442 0.022595632222066966 0.37343174523140904 chr4 191154276 4299166 0.022490556266708886 0.37977817698370453 chr5 180915260 4372211 0.024167176389653367 0.3863890823009805 chr6 171115067 4631538 0.027066804117255202 0.4195961217514212 chr7 159138663 4531790 0.028476989278212045 0.5619191267276163 chr8 146364022 3919191 0.02677701081485722 0.5373021082669729 chr9 141213431 3910068 0.027689065921781903 0.4614863784157423 chr10 135534747 4755672 0.035088212471448374 0.4951918600828805 chr11 135006516 3105430 0.02300207495170085 0.39205513769011463 chr12 133851895 6204308 0.046352037077995796 0.5634071156607188 chr13 115169878 3192402 0.02771907077994821 0.44001005691015144 chr14 107349540 4569478 0.04256634914318217 0.5605512463086495 chr15 102531392 3934280 0.038371467735461934 0.5436813284409093 chr16 90354753 2413534 0.026711754720861226 0.40474638828467635 chr17 81195210 2350453 0.028948173174254983 0.42492765435571533 chr18 78077248 1970801 0.025241681161713075 0.5859897893775577 chr19 59128983 1316282 0.02226119803210551 0.39539870826748513 chr20 63025520 2857993 0.045346599282322465 0.5414346397030687 chr21 48129895 1168865 0.02428563370021896 0.3879732402065161 chr22 51304566 960002 0.018711823817006853 0.3371674803614995 chrMT 16571 34239 2.0661999879307222 2.893019829280877 chrX 155270560 4088458 0.02633118602779561 0.4172279780669053 chrY 59373566 220053 0.0037062453011496733 0.15888421633976865