BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714106.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 = 1,019,196 number of mapped reads = 85,719 (8.41%) number of supplementary alignments = 2,330 (0.23%) number of secondary alignments = 0 number of mapped bases = 7,926,210 bp number of sequenced bases = 7,845,375 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 78,054 duplication rate = 35.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.2672 >>>>>>> ACTG content number of A's = 1,105,645 bp (14.09%) number of C's = 713,013 bp (9.09%) number of T's = 957,963 bp (12.21%) number of G's = 5,068,447 bp (64.6%) number of N's = 307 bp (0%) GC percentage = 73.69% >>>>>>> Mismatches and indels general error rate = 0.0335 number of mismatches = 222,733 number of insertions = 8,198 mapped reads with insertion percentage = 7.62% number of deletions = 13,168 mapped reads with deletion percentage = 14.46% homopolymer indels = 38.68% >>>>>>> Coverage mean coverageData = 0.0026X std coverageData = 5.1815X There is a 0.01% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 213861 8.580159164377769E-4 0.20808332375062602 chr2 243199373 4643684 0.019094144621828447 18.464846214406776 chr3 198022430 162656 8.214018987647005E-4 0.15301189364593334 chr4 191154276 143755 7.520365382775952E-4 0.14760323727796018 chr5 180915260 188707 0.0010430684509421704 0.2085923518639542 chr6 171115067 153794 8.987753252611005E-4 0.18396215067389998 chr7 159138663 223004 0.0014013187983111307 0.4427766765476408 chr8 146364022 202303 0.0013821907681656903 0.3847691356506281 chr9 141213431 151830 0.001075181014474466 0.34449461753655475 chr10 135534747 116592 8.60236969343367E-4 0.19088909336647839 chr11 135006516 135696 0.0010051070423889763 0.22404035637090988 chr12 133851895 179634 0.0013420355386078023 0.30076582339948016 chr13 115169878 81340 7.062610589897474E-4 0.19417707405187906 chr14 107349540 147720 0.001376065514579755 0.3149645233459738 chr15 102531392 67580 6.591152102957892E-4 0.12593767308002396 chr16 90354753 50625 5.60291498998398E-4 0.1137578578522908 chr17 81195210 35549 4.378213936511772E-4 0.16943746499479637 chr18 78077248 86627 0.0011095037570996356 0.2355345042202875 chr19 59128983 18304 3.095605415706203E-4 0.08346782673866159 chr20 63025520 51844 8.225874217301182E-4 0.14746545717247916 chr21 48129895 34591 7.187009238229171E-4 0.18857549762906747 chr22 51304566 36052 7.027054862914151E-4 0.16276514655735994 chrMT 16571 16793 1.013396898195643 9.137843345771046 chrX 155270560 765317 0.0049289253545553 0.49015717463681735 chrY 59373566 18352 3.0909378089232506E-4 0.11868093612091413