BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506020.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 5,372,028 number of mapped reads = 3,562,015 (66.31%) number of supplementary alignments = 143 (0%) number of secondary alignments = 0 number of mapped bases = 164,557,399 bp number of sequenced bases = 164,523,803 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 177,344 duplication rate = 3.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2534 >>>>>>> ACTG content number of A's = 48,338,053 bp (29.38%) number of C's = 33,477,884 bp (20.35%) number of T's = 48,058,184 bp (29.21%) number of G's = 34,113,631 bp (20.73%) number of N's = 536,051 bp (0.33%) GC percentage = 41.08% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,311,257 number of insertions = 7,339 mapped reads with insertion percentage = 0.21% number of deletions = 24,137 mapped reads with deletion percentage = 0.68% homopolymer indels = 45.36% >>>>>>> Coverage mean coverageData = 0.0532X std coverageData = 0.4682X There is a 4.29% of reference with a coverageData >= 1X There is a 0.73% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 16426906 0.06590517581900027 0.9229604599774831 chr2 243199373 10082103 0.04145612250406583 0.3799927203638499 chr3 198022430 8899966 0.04494423182262736 0.2544934694487526 chr4 191154276 7370826 0.03855956641011787 0.2446007541563229 chr5 180915260 12086583 0.0668079796032684 0.31345552086352885 chr6 171115067 10878139 0.06357206989843857 0.3763734774299657 chr7 159138663 10622868 0.06675227628373377 0.6617888176321645 chr8 146364022 9831972 0.0671747869841948 0.5587349897758386 chr9 141213431 8125693 0.05754192743889921 0.37282490267556434 chr10 135534747 5232627 0.03860727315925856 0.5094038207773872 chr11 135006516 7891227 0.05845071211229538 0.33216590973074833 chr12 133851895 4933454 0.03685755812422379 0.24984443530849737 chr13 115169878 5228771 0.045400508282209 0.25332400598662663 chr14 107349540 5664102 0.052763169735054294 0.7724016933229437 chr15 102531392 5372646 0.052400010330494684 0.2719656572658644 chr16 90354753 5134761 0.05682889753458791 0.340323752541368 chr17 81195210 2632740 0.03242481914881432 0.23312488206137894 chr18 78077248 4929273 0.06313328307882983 0.4856219709467335 chr19 59128983 4220771 0.07138243862574128 0.6655685045037053 chr20 63025520 3750295 0.05950438806375576 0.29974204237861385 chr21 48129895 2578444 0.053572608043296166 0.29964567895288097 chr22 51304566 1305443 0.025444967217927543 0.1892102264735953 chrMT 16571 11031 0.6656810089916119 1.0034600928664734 chrX 155270560 10842994 0.06983290328829883 0.35273642961670204 chrY 59373566 503764 0.008484651233513581 0.1470535985163329