BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818791.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 449,915 number of mapped reads = 432,247 (96.07%) number of supplementary alignments = 3,622 (0.81%) number of secondary alignments = 0 number of mapped bases = 29,289,328 bp number of sequenced bases = 29,277,952 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 172,140 duplication rate = 34.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6773 >>>>>>> ACTG content number of A's = 8,488,728 bp (28.99%) number of C's = 6,623,784 bp (22.62%) number of T's = 8,179,714 bp (27.94%) number of G's = 5,984,003 bp (20.44%) number of N's = 1,723 bp (0.01%) GC percentage = 43.06% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 150,759 number of insertions = 3,266 mapped reads with insertion percentage = 0.75% number of deletions = 7,441 mapped reads with deletion percentage = 1.71% homopolymer indels = 42.26% >>>>>>> Coverage mean coverageData = 0.0095X std coverageData = 0.1846X There is a 0.49% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 2467788 0.009900829896026617 0.21306255925458858 chr2 243199373 2589252 0.01064662284306136 0.23705664105515448 chr3 198022430 2003678 0.010118439613128674 0.17520900857483868 chr4 191154276 1949013 0.010196020935466807 0.17862061987792283 chr5 180915260 1836105 0.010148978035352021 0.1743331791016556 chr6 171115067 1735737 0.010143683022372308 0.177390202603256 chr7 159138663 1577616 0.009913467728455153 0.18067525792053163 chr8 146364022 1520838 0.01039079125606428 0.17812452217549837 chr9 141213431 1296238 0.009179282670357326 0.17138838705196358 chr10 135534747 1368511 0.010097122917121762 0.19191853193090982 chr11 135006516 1368261 0.010134777494739587 0.17746416527343048 chr12 133851895 1299055 0.009705167043021693 0.17382664799905798 chr13 115169878 948759 0.00823790922136776 0.1556575741775269 chr14 107349540 890576 0.008296039275063498 0.16179662809556056 chr15 102531392 865900 0.008445218416619176 0.16185213453708847 chr16 90354753 865327 0.009576994804025418 0.19826101295020854 chr17 81195210 790639 0.009737507914567867 0.18092382173979812 chr18 78077248 751238 0.009621727446131299 0.1855535929929566 chr19 59128983 575145 0.009726955729984397 0.20696984728064138 chr20 63025520 634843 0.01007279273538719 0.18165689509471497 chr21 48129895 367125 0.007627795572793168 0.15117658562966343 chr22 51304566 359117 0.006999708369036783 0.15729742562079974 chrMT 16571 59105 3.5667732786192747 4.630972200672088 chrX 155270560 896397 0.00577312917529247 0.13319337796615868 chrY 59373566 273065 0.004599100549224212 0.21150308261979797