BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818783.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 = 2,067,533 number of mapped reads = 2,011,507 (97.29%) number of supplementary alignments = 13,843 (0.67%) number of secondary alignments = 0 number of mapped bases = 136,701,983 bp number of sequenced bases = 136,645,371 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 837,535 duplication rate = 35.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5942 >>>>>>> ACTG content number of A's = 39,394,237 bp (28.83%) number of C's = 29,913,075 bp (21.89%) number of T's = 38,444,569 bp (28.13%) number of G's = 28,884,632 bp (21.14%) number of N's = 8,858 bp (0.01%) GC percentage = 43.03% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 703,535 number of insertions = 15,576 mapped reads with insertion percentage = 0.77% number of deletions = 34,089 mapped reads with deletion percentage = 1.68% homopolymer indels = 41.22% >>>>>>> Coverage mean coverageData = 0.0442X std coverageData = 0.5364X There is a 2.22% of reference with a coverageData >= 1X There is a 1% of reference with a coverageData >= 2X There is a 0.51% of reference with a coverageData >= 3X There is a 0.27% of reference with a coverageData >= 4X There is a 0.15% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% 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% 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 10882539 0.043661030637913635 0.8371393186537726 chr2 243199373 12098575 0.049747558354108094 0.842064131115193 chr3 198022430 9117026 0.046040370275225895 0.3741859106940782 chr4 191154276 9055848 0.047374551014490514 0.438345363742324 chr5 180915260 8308102 0.045922615925267994 0.38681198759378377 chr6 171115067 8149547 0.04762612166700668 0.4199260858551148 chr7 159138663 7585460 0.04766572658713364 0.46863501152700815 chr8 146364022 7091505 0.048451148739271456 0.4401474689265795 chr9 141213431 5883273 0.041662276444511856 0.44422653493076203 chr10 135534747 6778499 0.050012997773921396 0.5765333648452573 chr11 135006516 6413124 0.0475023294431211 0.44225115156811795 chr12 133851895 6300968 0.04707417851648645 0.430091733960317 chr13 115169878 4302107 0.03735444609917882 0.33608131639075345 chr14 107349540 4093502 0.038132459626748286 0.3809587109655242 chr15 102531392 3978049 0.03879835163068887 0.3484122126520637 chr16 90354753 4200250 0.046486209751467084 0.5691981310216807 chr17 81195210 3769197 0.04642142067247563 0.41914719261876887 chr18 78077248 3591465 0.04599886768550039 0.592353224602955 chr19 59128983 2904374 0.049119295692943 0.6786230221595877 chr20 63025520 3084498 0.04894046094344005 0.4145330710856665 chr21 48129895 1860952 0.03866519966436661 0.3758455810980784 chr22 51304566 1695663 0.033050917924147334 0.3529234665655101 chrMT 16571 6544 0.39490676483012493 1.0810361629446954 chrX 155270560 4260358 0.027438285789656455 0.3371654385875565 chrY 59373566 1290558 0.02173623864869427 0.9480673358846926