BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472729.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 = 15,898,008 number of mapped reads = 15,761,149 (99.14%) number of supplementary alignments = 61,141 (0.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,903,656 number of mapped paired reads (second in pair) = 7,857,493 number of mapped paired reads (both in pair) = 15,681,100 number of mapped paired reads (singletons) = 80,049 number of mapped bases = 1,554,389,347 bp number of sequenced bases = 1,554,188,299 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,867,475 duplication rate = 47.52% >>>>>>> Insert size mean insert size = 23,050.6051 std insert size = 1,477,391.2234 median insert size = 227 >>>>>>> Mapping quality mean mapping quality = 55.3077 >>>>>>> ACTG content number of A's = 420,706,389 bp (27.07%) number of C's = 358,412,988 bp (23.06%) number of T's = 419,174,086 bp (26.97%) number of G's = 355,593,002 bp (22.88%) number of N's = 301,834 bp (0.02%) GC percentage = 45.94% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 9,015,606 number of insertions = 90,283 mapped reads with insertion percentage = 0.57% number of deletions = 81,727 mapped reads with deletion percentage = 0.51% homopolymer indels = 44.92% >>>>>>> Coverage mean coverageData = 0.5021X std coverageData = 17.4841X There is a 4.36% of reference with a coverageData >= 1X There is a 1.92% of reference with a coverageData >= 2X There is a 0.87% of reference with a coverageData >= 3X There is a 0.64% of reference with a coverageData >= 4X There is a 0.49% of reference with a coverageData >= 5X There is a 0.44% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.34% of reference with a coverageData >= 10X There is a 0.33% of reference with a coverageData >= 11X There is a 0.32% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.29% of reference with a coverageData >= 15X There is a 0.28% of reference with a coverageData >= 16X There is a 0.28% of reference with a coverageData >= 17X There is a 0.27% of reference with a coverageData >= 18X There is a 0.26% of reference with a coverageData >= 19X There is a 0.26% of reference with a coverageData >= 20X There is a 0.25% of reference with a coverageData >= 21X There is a 0.25% of reference with a coverageData >= 22X There is a 0.24% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.23% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.22% of reference with a coverageData >= 29X There is a 0.21% of reference with a coverageData >= 30X There is a 0.21% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 171057578 0.6862874696709381 21.66230598709194 chr2 243199373 108080186 0.44440980528350293 20.75386707325171 chr3 198022430 175642095 0.8869808081842042 22.039004052739518 chr4 191154276 56021802 0.2930711421804658 13.237965484827939 chr5 180915260 66309624 0.3665231114279691 11.160740991102388 chr6 171115067 96493985 0.5639128493576782 16.275188772957176 chr7 159138663 58139404 0.36533801971177804 12.736409412346065 chr8 146364022 69046410 0.4717444154411116 18.77723639773398 chr9 141213431 72177702 0.5111249085081716 12.285132413559696 chr10 135534747 48242811 0.35594422882569 12.272761553228845 chr11 135006516 67818042 0.5023316207937697 15.811804720456971 chr12 133851895 98318863 0.7345347109206037 22.2020450935819 chr13 115169878 36907336 0.3204599730495503 12.601070096092279 chr14 107349540 49279997 0.459061091458799 31.74681220977852 chr15 102531392 42777776 0.417216377984998 13.00929545955132 chr16 90354753 55754076 0.6170574778728021 17.05783928144949 chr17 81195210 57485329 0.7079891658633557 17.749277248797313 chr18 78077248 21441988 0.27462530441646715 9.165345819487564 chr19 59128983 41805304 0.7070188235776015 17.925673507399257 chr20 63025520 33809340 0.5364388901511642 15.89196585890134 chr21 48129895 8120118 0.16871256419736633 8.14732944512409 chr22 51304566 21088908 0.4110532384193641 11.155682783091091 chrMT 16571 1699 0.10252851366845694 0.3569025092078087 chrX 155270560 95669648 0.6161480193025645 19.822314059254424 chrY 59373566 2899326 0.0488319330524968 2.348012204700809