BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695956.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 = 349,287,082 number of mapped reads = 344,385,903 (98.6%) number of supplementary alignments = 5,358,008 (1.53%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 173,291,127 number of mapped paired reads (second in pair) = 171,094,776 number of mapped paired reads (both in pair) = 341,058,108 number of mapped paired reads (singletons) = 3,327,795 number of mapped bases = 34,059,463,760 bp number of sequenced bases = 34,047,968,976 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 59,281,043 duplication rate = 13.82% >>>>>>> Insert size mean insert size = 80,894.8868 std insert size = 2,720,263.2824 median insert size = 321 >>>>>>> Mapping quality mean mapping quality = 53.9037 >>>>>>> ACTG content number of A's = 9,481,607,459 bp (27.85%) number of C's = 7,445,347,752 bp (21.87%) number of T's = 9,434,484,579 bp (27.71%) number of G's = 7,676,012,417 bp (22.54%) number of N's = 10,516,769 bp (0.03%) GC percentage = 44.41% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 166,803,691 number of insertions = 5,338,750 mapped reads with insertion percentage = 1.49% number of deletions = 4,396,865 mapped reads with deletion percentage = 1.23% homopolymer indels = 40.69% >>>>>>> Coverage mean coverageData = 11.0022X std coverageData = 41.0453X There is a 87.41% of reference with a coverageData >= 1X There is a 81% of reference with a coverageData >= 2X There is a 74.07% of reference with a coverageData >= 3X There is a 67.21% of reference with a coverageData >= 4X There is a 60.73% of reference with a coverageData >= 5X There is a 54.78% of reference with a coverageData >= 6X There is a 49.4% of reference with a coverageData >= 7X There is a 44.57% of reference with a coverageData >= 8X There is a 40.26% of reference with a coverageData >= 9X There is a 36.43% of reference with a coverageData >= 10X There is a 33.03% of reference with a coverageData >= 11X There is a 30% of reference with a coverageData >= 12X There is a 27.31% of reference with a coverageData >= 13X There is a 24.91% of reference with a coverageData >= 14X There is a 22.77% of reference with a coverageData >= 15X There is a 20.85% of reference with a coverageData >= 16X There is a 19.14% of reference with a coverageData >= 17X There is a 17.6% of reference with a coverageData >= 18X There is a 16.21% of reference with a coverageData >= 19X There is a 14.97% of reference with a coverageData >= 20X There is a 13.84% of reference with a coverageData >= 21X There is a 12.82% of reference with a coverageData >= 22X There is a 11.9% of reference with a coverageData >= 23X There is a 11.06% of reference with a coverageData >= 24X There is a 10.29% of reference with a coverageData >= 25X There is a 9.59% of reference with a coverageData >= 26X There is a 8.96% of reference with a coverageData >= 27X There is a 8.37% of reference with a coverageData >= 28X There is a 7.84% of reference with a coverageData >= 29X There is a 7.34% of reference with a coverageData >= 30X There is a 6.89% of reference with a coverageData >= 31X There is a 6.47% of reference with a coverageData >= 32X There is a 6.09% of reference with a coverageData >= 33X There is a 5.73% of reference with a coverageData >= 34X There is a 5.4% of reference with a coverageData >= 35X There is a 5.1% of reference with a coverageData >= 36X There is a 4.81% of reference with a coverageData >= 37X There is a 4.55% of reference with a coverageData >= 38X There is a 4.31% of reference with a coverageData >= 39X There is a 4.08% of reference with a coverageData >= 40X There is a 3.87% of reference with a coverageData >= 41X There is a 3.67% of reference with a coverageData >= 42X There is a 3.48% of reference with a coverageData >= 43X There is a 3.31% of reference with a coverageData >= 44X There is a 3.15% of reference with a coverageData >= 45X There is a 2.99% of reference with a coverageData >= 46X There is a 2.85% of reference with a coverageData >= 47X There is a 2.72% of reference with a coverageData >= 48X There is a 2.59% of reference with a coverageData >= 49X There is a 2.47% of reference with a coverageData >= 50X There is a 2.36% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3010636856 12.078753681420116 33.886023603537325 chr2 243199373 2688576604 11.05503098480439 84.16500311359663 chr3 198022430 1976455587 9.980968251929845 18.123172381502034 chr4 191154276 1906011611 9.971064476737105 24.367688039075343 chr5 180915260 1719360439 9.503678346425835 19.278722590421413 chr6 171115067 2158472111 12.614155777410296 30.81206386932978 chr7 159138663 1692910224 10.637956811287273 23.27244951784017 chr8 146364022 1486953634 10.159283775352934 28.787821460016055 chr9 141213431 1280452151 9.067495506146296 59.45361605502387 chr10 135534747 1547428500 11.41720875459339 59.601164264953 chr11 135006516 1815010353 13.443872242433098 27.773658948332848 chr12 133851895 1848793060 13.812229255327315 20.533540212570184 chr13 115169878 924456064 8.02689105913614 18.238955422534328 chr14 107349540 1128225645 10.509832133421344 41.57032891323379 chr15 102531392 1016204374 9.911153590892436 22.29513266372826 chr16 90354753 1241232186 13.737320337757993 62.020206920486466 chr17 81195210 1457921673 17.955759619317444 35.19096829825011 chr18 78077248 894803238 11.46048638906945 43.34008402409524 chr19 59128983 1236567435 20.913050965209397 37.55217831007715 chr20 63025520 952540831 15.113573533387745 22.97195124931169 chr21 48129895 432194237 8.979746101669242 25.192942757576223 chr22 51304566 609954654 11.888896087728332 24.400582482457693 chrMT 16571 22393065 1351.3405950153883 477.233084833287 chrX 155270560 764465211 4.923439517446192 12.501804992004109 chrY 59373566 247444017 4.167578834661876 73.29006103952857