BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472823.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 2,984,005 number of mapped reads = 2,196,367 (73.6%) number of supplementary alignments = 16,625 (0.56%) number of secondary alignments = 0 number of mapped bases = 134,988,562 bp number of sequenced bases = 134,920,158 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 243,369 duplication rate = 7.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.1888 >>>>>>> ACTG content number of A's = 35,754,925 bp (26.5%) number of C's = 26,172,900 bp (19.4%) number of T's = 40,449,515 bp (29.98%) number of G's = 32,540,269 bp (24.12%) number of N's = 2,549 bp (0%) GC percentage = 43.52% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 1,240,569 number of insertions = 10,061 mapped reads with insertion percentage = 0.45% number of deletions = 37,644 mapped reads with deletion percentage = 1.69% homopolymer indels = 46.4% >>>>>>> Coverage mean coverageData = 0.0436X std coverageData = 0.4162X There is a 2.86% of reference with a coverageData >= 1X There is a 0.69% of reference with a coverageData >= 2X There is a 0.3% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.04% 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 0.02% 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 0.01% 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 10870830 0.043614053824162786 0.48127508355729703 chr2 243199373 11680677 0.04802922333192035 0.5010092447073935 chr3 198022430 9269655 0.04681113649600199 0.3365328387147479 chr4 191154276 6963949 0.036431039606982164 0.3280551827166798 chr5 180915260 7513054 0.04152802809447915 0.3320514041692388 chr6 171115067 8551615 0.04997581539678209 0.38680940628723354 chr7 159138663 8061880 0.05065946796348289 0.6305757432257476 chr8 146364022 6740623 0.04605382462091674 0.4027532478435966 chr9 141213431 5813570 0.041168676087191734 0.42535412002712203 chr10 135534747 6458590 0.04765265102092233 0.39829714733959265 chr11 135006516 5581209 0.04134029353072114 0.425304824722207 chr12 133851895 6706397 0.05010311583560322 0.383826607729999 chr13 115169878 4648905 0.04036563275685679 0.33260200168578763 chr14 107349540 4361582 0.04062972230714729 0.37637232132302273 chr15 102531392 3997962 0.038992565320872655 0.3763131488970991 chr16 90354753 4013883 0.04442359551356419 0.35506315073563943 chr17 81195210 3588720 0.0441986663991632 0.37839284046098465 chr18 78077248 2901696 0.03716442464775398 0.5930812302033266 chr19 59128983 2835496 0.04795441856322812 0.4352602656981488 chr20 63025520 3547032 0.05627929765593366 0.41144827520569716 chr21 48129895 1926940 0.040036239430815294 0.3387098442713285 chr22 51304566 1550990 0.030231032458202647 0.2935261626380353 chrMT 16571 191593 11.561945567557782 9.044334180523272 chrX 155270560 6729481 0.04334035376699871 0.36536039502047934 chrY 59373566 482233 0.008122015106857486 0.15418421290661782