BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818832.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 = 2,620,218 number of mapped reads = 2,582,958 (98.58%) number of supplementary alignments = 39,190 (1.5%) number of secondary alignments = 0 number of mapped bases = 239,550,515 bp number of sequenced bases = 239,399,114 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 706,684 duplication rate = 23.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3269 >>>>>>> ACTG content number of A's = 69,158,209 bp (28.89%) number of C's = 50,208,163 bp (20.97%) number of T's = 66,086,728 bp (27.61%) number of G's = 53,942,354 bp (22.53%) number of N's = 3,660 bp (0%) GC percentage = 43.5% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 1,421,589 number of insertions = 33,854 mapped reads with insertion percentage = 1.27% number of deletions = 75,957 mapped reads with deletion percentage = 2.87% homopolymer indels = 40.51% >>>>>>> Coverage mean coverageData = 0.0774X std coverageData = 0.8963X There is a 4.86% of reference with a coverageData >= 1X There is a 1.57% of reference with a coverageData >= 2X There is a 0.59% of reference with a coverageData >= 3X There is a 0.25% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% 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% 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 22685252 0.09101382339183821 1.4098033455955827 chr2 243199373 17702327 0.07278936117980864 1.226971800336372 chr3 198022430 14466700 0.07305586543908182 0.39442554059773116 chr4 191154276 11745157 0.06144333909642701 0.5114796413218006 chr5 180915260 11814779 0.06530559666442731 0.39668476933282176 chr6 171115067 11656284 0.06811956541500813 0.42085188295277937 chr7 159138663 22569342 0.14182186512400197 2.0047416460946423 chr8 146364022 21318902 0.14565671063616986 0.7214527847981282 chr9 141213431 8711584 0.06169090247513354 0.6693814302695821 chr10 135534747 11552071 0.08523327969911657 1.2674522793373697 chr11 135006516 10342209 0.07660525807509913 0.49705521892185994 chr12 133851895 9408073 0.07028718569879044 0.392937719812019 chr13 115169878 7257004 0.063011302312919 0.36331813067551744 chr14 107349540 7095482 0.06609699491958698 0.4120194410678709 chr15 102531392 6665793 0.06501221596601361 0.370773630536551 chr16 90354753 6507491 0.07202156814041648 0.8855513437168527 chr17 81195210 6026963 0.07422806099029733 0.5740291682904373 chr18 78077248 4514408 0.05781976331952684 0.808254692771137 chr19 59128983 4246433 0.07181643898728987 1.3230431474045725 chr20 63025520 8721007 0.13837263064231758 0.5997364681909726 chr21 48129895 2295570 0.04769530455032158 0.3913428208630034 chr22 51304566 1602726 0.031239441729221527 0.3183399560004738 chrMT 16571 98501 5.944179590851488 4.942527830660089 chrX 155270560 9660644 0.06221813072613379 0.42891244811235324 chrY 59373566 885813 0.014919316114514665 1.0740189719760067