BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714092.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 561,278 number of mapped reads = 307,186 (54.73%) number of supplementary alignments = 8,551 (1.52%) number of secondary alignments = 0 number of mapped bases = 39,246,489 bp number of sequenced bases = 38,320,037 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 261,196 duplication rate = 43.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.8313 >>>>>>> ACTG content number of A's = 10,050,172 bp (26.23%) number of C's = 7,807,466 bp (20.37%) number of T's = 9,553,100 bp (24.93%) number of G's = 10,908,978 bp (28.47%) number of N's = 321 bp (0%) GC percentage = 48.84% >>>>>>> Mismatches and indels general error rate = 0.0468 number of mismatches = 1,683,384 number of insertions = 41,264 mapped reads with insertion percentage = 12.68% number of deletions = 144,551 mapped reads with deletion percentage = 43.52% homopolymer indels = 29.54% >>>>>>> Coverage mean coverageData = 0.0127X std coverageData = 4.2291X There is a 0.05% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% 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 3557946 0.014274572258738726 2.136296905751211 chr2 243199373 7340721 0.030183963508820393 13.51221985102639 chr3 198022430 3286908 0.016598665110815983 2.7307265593354986 chr4 191154276 1138330 0.005955032886630273 1.2182023875365215 chr5 180915260 1596118 0.008822461963683992 1.9371726207332407 chr6 171115067 1811168 0.010584503350602084 1.5206153148189843 chr7 159138663 1298113 0.008157118927158513 1.4642547935736179 chr8 146364022 1977806 0.013512924644828358 3.3523208110769653 chr9 141213431 2523207 0.01786803834544605 2.5546964440929396 chr10 135534747 948939 0.007001444434023992 0.9532854767515857 chr11 135006516 1074502 0.007958889924987028 1.1275316588022664 chr12 133851895 1050641 0.007849279982177316 1.0983361820131294 chr13 115169878 2025484 0.01758692494230132 2.929705280317992 chr14 107349540 1122667 0.010458051333988017 2.244602510797146 chr15 102531392 1209214 0.011793597808561889 1.3442296968197691 chr16 90354753 547784 0.006062591970120266 0.8519125414704174 chr17 81195210 687944 0.008472716555570211 1.5384486394418984 chr18 78077248 658705 0.008436580654072233 1.3736376779504416 chr19 59128983 363972 0.006155559956104775 0.926263896404229 chr20 63025520 1048998 0.016644019755806854 2.2275326074142416 chr21 48129895 312842 0.006499951849053483 1.4005367044029173 chr22 51304566 357457 0.006967352574427781 2.2073800771134757 chrMT 16571 273110 16.48120210005431 119.41554687037457 chrX 155270560 2972448 0.019143667672738476 1.891997465710493 chrY 59373566 61465 0.0010352250023183717 0.1989760781955614