BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046490.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 9,548,528 number of mapped reads = 9,469,759 (99.18%) number of supplementary alignments = 48,818 (0.51%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,761,587 number of mapped paired reads (second in pair) = 4,708,172 number of mapped paired reads (both in pair) = 9,409,210 number of mapped paired reads (singletons) = 60,549 number of mapped bases = 927,279,372 bp number of sequenced bases = 927,039,428 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,653,535 duplication rate = 26.97% >>>>>>> Insert size mean insert size = 19,214.5512 std insert size = 1,475,965.9846 median insert size = 156 >>>>>>> Mapping quality mean mapping quality = 52.3847 >>>>>>> ACTG content number of A's = 256,655,982 bp (27.69%) number of C's = 206,453,543 bp (22.27%) number of T's = 257,056,018 bp (27.73%) number of G's = 206,793,855 bp (22.31%) number of N's = 80,030 bp (0.01%) GC percentage = 44.58% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 3,557,311 number of insertions = 65,646 mapped reads with insertion percentage = 0.68% number of deletions = 86,273 mapped reads with deletion percentage = 0.89% homopolymer indels = 49.34% >>>>>>> Coverage mean coverageData = 0.2995X std coverageData = 60.365X There is a 2.14% of reference with a coverageData >= 1X There is a 1.24% of reference with a coverageData >= 2X There is a 0.6% of reference with a coverageData >= 3X There is a 0.39% of reference with a coverageData >= 4X There is a 0.24% of reference with a coverageData >= 5X There is a 0.17% of reference with a coverageData >= 6X There is a 0.13% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% 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 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 159371630 0.6394031411460355 84.57561807254541 chr2 243199373 139690475 0.5743866576498122 83.94108469916928 chr3 198022430 63410418 0.32021836112202035 66.65810563785973 chr4 191154276 38013611 0.19886351378297182 43.82192031223163 chr5 180915260 87224853 0.48213098773425744 154.60140640262205 chr6 171115067 40831781 0.23862177490191439 42.06711114450581 chr7 159138663 31086085 0.19533961398180152 19.590940441775246 chr8 146364022 18206880 0.12439450454565945 15.385593946517483 chr9 141213431 5852927 0.041447381871204586 3.354393322410634 chr10 135534747 38301400 0.2825946913819819 25.89949199447781 chr11 135006516 25633265 0.18986687279597675 18.02471635487069 chr12 133851895 22570753 0.16862482970450288 17.913413553702526 chr13 115169878 12662823 0.10994908755568883 14.083779163110657 chr14 107349540 31812448 0.2963445208987388 20.792022966817793 chr15 102531392 6648813 0.06484660814904376 3.7501217296211915 chr16 90354753 78077372 0.8641202527552702 92.85845969185658 chr17 81195210 12748593 0.15701163898707818 16.285651263145486 chr18 78077248 10122386 0.12964578362188175 15.945097769419787 chr19 59128983 19114543 0.32326859063346314 20.233443428388913 chr20 63025520 55669802 0.8832898483027193 99.36941666830019 chr21 48129895 2007262 0.04170509825546056 2.4034065884539038 chr22 51304566 5199598 0.10134766562492703 5.517231201319319 chrMT 16571 269103 16.239394122261782 7.394714689386199 chrX 155270560 22591385 0.14549689909020744 24.773303554043686 chrY 59373566 161166 0.0027144402948611843 0.12304319635716207