BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695939.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 14,508,370 number of mapped reads = 14,411,404 (99.33%) number of supplementary alignments = 35,677 (0.25%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,241,103 number of mapped paired reads (second in pair) = 7,170,301 number of mapped paired reads (both in pair) = 14,330,084 number of mapped paired reads (singletons) = 81,320 number of mapped bases = 1,430,316,346 bp number of sequenced bases = 1,430,056,367 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 414,848 duplication rate = 2.79% >>>>>>> Insert size mean insert size = 29,768.3458 std insert size = 1,689,151.4291 median insert size = 328 >>>>>>> Mapping quality mean mapping quality = 54.327 >>>>>>> ACTG content number of A's = 425,405,406 bp (29.75%) number of C's = 288,318,926 bp (20.16%) number of T's = 425,581,465 bp (29.76%) number of G's = 290,121,915 bp (20.29%) number of N's = 628,655 bp (0.04%) GC percentage = 40.45% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 9,211,528 number of insertions = 90,191 mapped reads with insertion percentage = 0.62% number of deletions = 116,262 mapped reads with deletion percentage = 0.79% homopolymer indels = 45.17% >>>>>>> Coverage mean coverageData = 0.462X std coverageData = 1.509X There is a 18.94% of reference with a coverageData >= 1X There is a 9.2% of reference with a coverageData >= 2X There is a 5.38% of reference with a coverageData >= 3X There is a 3.45% of reference with a coverageData >= 4X There is a 2.34% of reference with a coverageData >= 5X There is a 1.65% of reference with a coverageData >= 6X There is a 1.19% of reference with a coverageData >= 7X There is a 0.88% of reference with a coverageData >= 8X There is a 0.66% of reference with a coverageData >= 9X There is a 0.5% of reference with a coverageData >= 10X There is a 0.38% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.24% of reference with a coverageData >= 13X There is a 0.19% of reference with a coverageData >= 14X There is a 0.15% of reference with a coverageData >= 15X There is a 0.12% of reference with a coverageData >= 16X There is a 0.1% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% 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 114516945 0.4594449736596644 1.4849149624513196 chr2 243199373 163276470 0.6713687950174115 1.8364459834696432 chr3 198022430 119804653 0.6050054683199272 1.7126318568354812 chr4 191154276 96085558 0.5026597364737998 1.4747651321556188 chr5 180915260 86792131 0.47973913864424705 1.4515923486048998 chr6 171115067 80431796 0.47004508375641757 1.6613627930339314 chr7 159138663 108816983 0.6837872139217357 1.7996150026619449 chr8 146364022 76821196 0.524863931383356 1.5155569472105312 chr9 141213431 73029897 0.5171597098295841 1.4407243898466553 chr10 135534747 79798880 0.588770641966816 1.6724799399839887 chr11 135006516 69421823 0.5142109066794969 1.678959413743001 chr12 133851895 66922129 0.4999714722006737 1.5904791940146625 chr13 115169878 35310133 0.30659173746802093 1.6931431692756336 chr14 107349540 62469949 0.5819302905256977 1.6658225976668604 chr15 102531392 31277564 0.3050535391151229 1.3306168967182392 chr16 90354753 30470553 0.337232430927015 1.1808272646720908 chr17 81195210 35101933 0.43231531761541103 1.4315772991987536 chr18 78077248 21487977 0.2752143236400955 1.0476365063370754 chr19 59128983 10979116 0.1856807853434584 0.9250500011438766 chr20 63025520 6888806 0.10930185105969772 0.5951934470454254 chr21 48129895 22961311 0.477069625853121 1.5043505377438386 chr22 51304566 6847829 0.13347406544672846 0.620774494412433 chrMT 16571 2589 0.15623679922756623 0.47814481967038547 chrX 155270560 20444342 0.1316691457801144 0.7083424084704866 chrY 59373566 10355783 0.17441739982402268 0.8344762301596736