BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472735.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 = 15,388,404 number of mapped reads = 14,651,886 (95.21%) number of supplementary alignments = 69,215 (0.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,153,273 number of mapped paired reads (second in pair) = 7,498,613 number of mapped paired reads (both in pair) = 14,115,372 number of mapped paired reads (singletons) = 536,514 number of mapped bases = 1,414,954,293 bp number of sequenced bases = 1,414,762,547 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,563,386 duplication rate = 44.4% >>>>>>> Insert size mean insert size = 33,553.342 std insert size = 1,796,451.2781 median insert size = 250 >>>>>>> Mapping quality mean mapping quality = 54.4534 >>>>>>> ACTG content number of A's = 408,730,579 bp (28.89%) number of C's = 322,376,383 bp (22.79%) number of T's = 367,174,661 bp (25.95%) number of G's = 316,236,513 bp (22.35%) number of N's = 244,411 bp (0.02%) GC percentage = 45.14% >>>>>>> Mismatches and indels general error rate = 0.0183 number of mismatches = 25,753,524 number of insertions = 77,283 mapped reads with insertion percentage = 0.52% number of deletions = 76,110 mapped reads with deletion percentage = 0.51% homopolymer indels = 44.57% >>>>>>> Coverage mean coverageData = 0.4571X std coverageData = 14.0154X There is a 4.28% of reference with a coverageData >= 1X There is a 1.68% of reference with a coverageData >= 2X There is a 0.78% of reference with a coverageData >= 3X There is a 0.59% of reference with a coverageData >= 4X There is a 0.48% of reference with a coverageData >= 5X There is a 0.44% 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 0.3% of reference with a coverageData >= 15X There is a 0.29% of reference with a coverageData >= 16X There is a 0.29% of reference with a coverageData >= 17X There is a 0.28% of reference with a coverageData >= 18X There is a 0.27% of reference with a coverageData >= 19X There is a 0.27% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.26% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.25% of reference with a coverageData >= 24X There is a 0.24% of reference with a coverageData >= 25X There is a 0.24% of reference with a coverageData >= 26X There is a 0.23% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.22% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.2% of reference with a coverageData >= 36X There is a 0.2% 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 0.19% of reference with a coverageData >= 40X There is a 0.19% 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 0.18% of reference with a coverageData >= 44X There is a 0.18% 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 0.17% 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 146056466 0.5859823554862879 18.123153511184228 chr2 243199373 82256340 0.33822595422563034 9.673794273780263 chr3 198022430 239766574 1.2108051294997237 26.111360532966447 chr4 191154276 48405635 0.25322810461221384 8.51509745839997 chr5 180915260 52665853 0.2911078534779211 9.698160667990075 chr6 171115067 71017166 0.4150257908030974 11.747657289420145 chr7 159138663 55267800 0.3472933538470158 9.302652529592658 chr8 146364022 79418308 0.5426081281095159 18.73679032360695 chr9 141213431 62149525 0.4401105798498728 10.014905537305088 chr10 135534747 34464167 0.25428288880046385 9.395832834138597 chr11 135006516 58430035 0.43279418454143354 12.332012148869858 chr12 133851895 82249438 0.6144809380547059 14.11217812512191 chr13 115169878 29135801 0.25298108764168353 9.003820815612242 chr14 107349540 40703295 0.3791659936316448 19.63962517781717 chr15 102531392 29154371 0.28434580308828733 7.494198334689979 chr16 90354753 50003247 0.5534102561267585 18.879108622665434 chr17 81195210 71837849 0.8847547657060065 18.881805507006128 chr18 78077248 25806896 0.33053029737933387 10.582324015479493 chr19 59128983 26879961 0.45459873713708215 10.282774706190105 chr20 63025520 29160690 0.4626806728449047 10.155909052780869 chr21 48129895 7875450 0.1636290708716485 7.673174989060332 chr22 51304566 17158077 0.334435671865931 12.411214152581815 chrMT 16571 2004 0.1209341620903989 0.5423432885005312 chrX 155270560 72830228 0.4690536828101863 12.765230119854392 chrY 59373566 2259117 0.038049205264174296 1.3990400754857275