BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094163.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 25,022 number of mapped reads = 719 (2.87%) number of supplementary alignments = 21 (0.08%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 262 number of mapped paired reads (second in pair) = 457 number of mapped paired reads (both in pair) = 450 number of mapped paired reads (singletons) = 269 number of mapped bases = 52,353 bp number of sequenced bases = 52,071 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 509 duplication rate = 22.08% >>>>>>> Insert size mean insert size = 290,076.5556 std insert size = 4,252,373.3185 median insert size = 31 >>>>>>> Mapping quality mean mapping quality = 6.9005 >>>>>>> ACTG content number of A's = 7,079 bp (13.59%) number of C's = 4,907 bp (9.42%) number of T's = 6,195 bp (11.9%) number of G's = 33,890 bp (65.08%) number of N's = 0 bp (0%) GC percentage = 74.51% >>>>>>> Mismatches and indels general error rate = 0.0341 number of mismatches = 1,322 number of insertions = 78 mapped reads with insertion percentage = 7.65% number of deletions = 56 mapped reads with deletion percentage = 7.23% homopolymer indels = 42.54% >>>>>>> Coverage mean coverageData = 0X std coverageData = 0.0372X There is a 0% of reference with a coverageData >= 1X There is a 0% 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 668 2.680033443126306E-6 0.002120724932664908 chr2 243199373 30946 1.272453938440047E-4 0.12562301941741774 chr3 198022430 694 3.504653487991234E-6 0.002436946838313997 chr4 191154276 268 1.4020089197481515E-6 0.00247189115126883 chr5 180915260 693 3.8305226435846265E-6 0.002299946837271514 chr6 171115067 347 2.0278751958177942E-6 0.0018772161409049022 chr7 159138663 465 2.921980059616311E-6 0.002013221697978772 chr8 146364022 655 4.4751434884728705E-6 0.0025057625643168193 chr9 141213431 365 2.5847399742025954E-6 0.001616495966851563 chr10 135534747 515 3.7997636133854297E-6 0.0025639706554564843 chr11 135006516 1094 8.103312583816324E-6 0.003992481477569212 chr12 133851895 685 5.117596579413388E-6 0.0029170840288427827 chr13 115169878 455 3.950685786087227E-6 0.002474141627161553 chr14 107349540 805 7.4988677175514676E-6 0.003928804160388192 chr15 102531392 459 4.476677737877586E-6 0.0026147492406641314 chr16 90354753 228 2.523386899192785E-6 0.001968149860276773 chr17 81195210 292 3.5962712578734633E-6 0.0026726888320090843 chr18 78077248 250 3.201957118160722E-6 0.0033533957634688857 chr19 59128983 173 2.925807129136654E-6 0.0020848073492566667 chr20 63025520 227 3.6017156224970456E-6 0.0023799914231018996 chr21 48129895 100 2.0777107450577235E-6 0.0014414251379019942 chr22 51304566 0 0.0 0.0 chrMT 16571 903 0.054492788606601894 0.3654501291714979 chrX 155270560 10880 7.00712356547178E-5 0.0521303561319783 chrY 59373566 186 3.1327072387735646E-6 0.0023575451550634126