BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472430.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 = 19,613,544 number of mapped reads = 19,338,231 (98.6%) number of supplementary alignments = 68,375 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,724,791 number of mapped paired reads (second in pair) = 9,613,440 number of mapped paired reads (both in pair) = 19,170,092 number of mapped paired reads (singletons) = 168,139 number of mapped bases = 1,892,128,093 bp number of sequenced bases = 1,891,912,049 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,650,304 duplication rate = 48.44% >>>>>>> Insert size mean insert size = 18,670.9045 std insert size = 1,353,165.0367 median insert size = 200 >>>>>>> Mapping quality mean mapping quality = 54.8566 >>>>>>> ACTG content number of A's = 508,808,238 bp (26.89%) number of C's = 438,463,899 bp (23.18%) number of T's = 509,419,403 bp (26.93%) number of G's = 434,982,382 bp (22.99%) number of N's = 238,127 bp (0.01%) GC percentage = 46.17% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 10,226,789 number of insertions = 102,208 mapped reads with insertion percentage = 0.52% number of deletions = 89,892 mapped reads with deletion percentage = 0.45% homopolymer indels = 44.37% >>>>>>> Coverage mean coverageData = 0.6112X std coverageData = 19.832X There is a 5% of reference with a coverageData >= 1X There is a 2.27% of reference with a coverageData >= 2X There is a 0.94% of reference with a coverageData >= 3X There is a 0.69% of reference with a coverageData >= 4X There is a 0.5% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.41% of reference with a coverageData >= 7X There is a 0.39% of reference with a coverageData >= 8X There is a 0.37% of reference with a coverageData >= 9X There is a 0.35% of reference with a coverageData >= 10X There is a 0.34% of reference with a coverageData >= 11X There is a 0.33% of reference with a coverageData >= 12X There is a 0.32% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.31% of reference with a coverageData >= 15X There is a 0.3% of reference with a coverageData >= 16X There is a 0.29% of reference with a coverageData >= 17X There is a 0.29% of reference with a coverageData >= 18X There is a 0.28% of reference with a coverageData >= 19X There is a 0.27% of reference with a coverageData >= 20X There is a 0.27% of reference with a coverageData >= 21X There is a 0.26% of reference with a coverageData >= 22X There is a 0.26% of reference with a coverageData >= 23X There is a 0.26% of reference with a coverageData >= 24X There is a 0.25% of reference with a coverageData >= 25X There is a 0.25% of reference with a coverageData >= 26X There is a 0.24% of reference with a coverageData >= 27X There is a 0.24% of reference with a coverageData >= 28X There is a 0.24% of reference with a coverageData >= 29X There is a 0.23% of reference with a coverageData >= 30X There is a 0.23% of reference with a coverageData >= 31X There is a 0.23% of reference with a coverageData >= 32X There is a 0.22% of reference with a coverageData >= 33X There is a 0.22% of reference with a coverageData >= 34X There is a 0.22% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.21% of reference with a coverageData >= 38X There is a 0.21% of reference with a coverageData >= 39X There is a 0.2% of reference with a coverageData >= 40X There is a 0.2% of reference with a coverageData >= 41X There is a 0.2% of reference with a coverageData >= 42X There is a 0.2% of reference with a coverageData >= 43X There is a 0.19% of reference with a coverageData >= 44X There is a 0.19% of reference with a coverageData >= 45X There is a 0.19% of reference with a coverageData >= 46X There is a 0.19% of reference with a coverageData >= 47X There is a 0.19% of reference with a coverageData >= 48X There is a 0.18% of reference with a coverageData >= 49X There is a 0.18% of reference with a coverageData >= 50X There is a 0.18% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 204256469 0.8194822872678018 26.462321532735153 chr2 243199373 153187831 0.6298857974440584 18.591564314247695 chr3 198022430 139203770 0.7029697090375066 21.933921961591192 chr4 191154276 46013666 0.24071481403847853 10.394251459835154 chr5 180915260 77603064 0.4289470329921312 15.822415571863443 chr6 171115067 153150066 0.895012161611695 21.150614714418893 chr7 159138663 105807654 0.6648771078339397 17.732238692052274 chr8 146364022 149054019 1.0183788130665061 26.372710422373213 chr9 141213431 71536149 0.506581764166611 13.88454898584529 chr10 135534747 38876856 0.28684051035266994 10.270681121229565 chr11 135006516 75316254 0.5578712511920536 19.39636609284852 chr12 133851895 85820923 0.6411633021706566 21.125934709500548 chr13 115169878 66786798 0.579898139685448 23.927472039667144 chr14 107349540 35219495 0.3280824025887768 10.838899157247225 chr15 102531392 25095120 0.24475547937552627 6.943764548260073 chr16 90354753 110597881 1.2240405438328186 32.50388641099709 chr17 81195210 75735447 0.9327575727681473 20.22272135678899 chr18 78077248 8579976 0.10989086090739264 3.646272867748019 chr19 59128983 40587440 0.686422088470556 17.287520338296584 chr20 63025520 74640978 1.1842976940134726 30.130208276624483 chr21 48129895 10263521 0.2132462786382559 8.195215382247776 chr22 51304566 26930238 0.5249091864455105 19.179427669356983 chrMT 16571 5322 0.3211634783658198 0.7848194587122221 chrX 155270560 117490594 0.7566830054583432 26.23528471149342 chrY 59373566 368562 0.006207509921165927 0.4895220354895089