BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777291.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 105,013,456 number of mapped reads = 103,303,951 (98.37%) number of supplementary alignments = 5,018,236 (4.78%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 51,798,689 number of mapped paired reads (second in pair) = 51,505,262 number of mapped paired reads (both in pair) = 102,787,226 number of mapped paired reads (singletons) = 516,725 number of mapped bases = 9,992,799,585 bp number of sequenced bases = 9,989,675,068 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,244,745 duplication rate = 12.8% >>>>>>> Insert size mean insert size = 147,566.567 std insert size = 3,690,342.5756 median insert size = 156 >>>>>>> Mapping quality mean mapping quality = 53.0067 >>>>>>> ACTG content number of A's = 2,920,633,365 bp (29.24%) number of C's = 2,078,355,465 bp (20.81%) number of T's = 2,853,386,397 bp (28.56%) number of G's = 2,137,141,067 bp (21.39%) number of N's = 158,774 bp (0%) GC percentage = 42.2% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 56,170,751 number of insertions = 2,268,718 mapped reads with insertion percentage = 2.15% number of deletions = 1,255,464 mapped reads with deletion percentage = 1.18% homopolymer indels = 46.57% >>>>>>> Coverage mean coverageData = 3.228X std coverageData = 29.2806X There is a 52.92% of reference with a coverageData >= 1X There is a 41.95% of reference with a coverageData >= 2X There is a 33.04% of reference with a coverageData >= 3X There is a 26.87% of reference with a coverageData >= 4X There is a 22.08% of reference with a coverageData >= 5X There is a 18.36% of reference with a coverageData >= 6X There is a 15.4% of reference with a coverageData >= 7X There is a 13.01% of reference with a coverageData >= 8X There is a 11.06% of reference with a coverageData >= 9X There is a 9.45% of reference with a coverageData >= 10X There is a 8.11% of reference with a coverageData >= 11X There is a 6.98% of reference with a coverageData >= 12X There is a 6.03% of reference with a coverageData >= 13X There is a 5.23% of reference with a coverageData >= 14X There is a 4.54% of reference with a coverageData >= 15X There is a 3.95% of reference with a coverageData >= 16X There is a 3.45% of reference with a coverageData >= 17X There is a 3.02% of reference with a coverageData >= 18X There is a 2.64% of reference with a coverageData >= 19X There is a 2.32% of reference with a coverageData >= 20X There is a 2.04% of reference with a coverageData >= 21X There is a 1.79% of reference with a coverageData >= 22X There is a 1.58% of reference with a coverageData >= 23X There is a 1.4% of reference with a coverageData >= 24X There is a 1.24% of reference with a coverageData >= 25X There is a 1.1% of reference with a coverageData >= 26X There is a 0.97% of reference with a coverageData >= 27X There is a 0.87% of reference with a coverageData >= 28X There is a 0.77% of reference with a coverageData >= 29X There is a 0.69% of reference with a coverageData >= 30X There is a 0.61% of reference with a coverageData >= 31X There is a 0.55% of reference with a coverageData >= 32X There is a 0.49% of reference with a coverageData >= 33X There is a 0.44% of reference with a coverageData >= 34X There is a 0.4% of reference with a coverageData >= 35X There is a 0.36% of reference with a coverageData >= 36X There is a 0.33% of reference with a coverageData >= 37X There is a 0.3% of reference with a coverageData >= 38X There is a 0.27% of reference with a coverageData >= 39X There is a 0.24% of reference with a coverageData >= 40X There is a 0.22% of reference with a coverageData >= 41X There is a 0.2% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.13% of reference with a coverageData >= 47X There is a 0.12% of reference with a coverageData >= 48X There is a 0.11% of reference with a coverageData >= 49X There is a 0.1% of reference with a coverageData >= 50X There is a 0.1% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 822677585 3.300603953159258 63.1124067633637 chr2 243199373 857230954 3.5248074179862297 20.01230653373205 chr3 198022430 670651008 3.38674264324501 6.991573483388195 chr4 191154276 655635705 3.4298772631170436 23.312130905014325 chr5 180915260 606293157 3.3512549300705756 6.097431753276722 chr6 171115067 580788197 3.3941382672047227 13.575740475680636 chr7 159138663 540169700 3.394333531632096 26.701217236674232 chr8 146364022 509896120 3.483753131626842 14.974965218998792 chr9 141213431 419290167 2.9691946724246083 25.646674829952126 chr10 135534747 509260840 3.757419047677862 46.278962082129524 chr11 135006516 473507040 3.5072902703451736 23.13166347220916 chr12 133851895 448791170 3.3528936590699745 5.998021040896503 chr13 115169878 312609654 2.7143352014317492 5.380493888249247 chr14 107349540 304453661 2.8360965589605693 5.934194161264756 chr15 102531392 284396636 2.7737518281230398 5.361249830097769 chr16 90354753 302477834 3.347669314086886 12.55332284645959 chr17 81195210 280901247 3.4595790441332683 14.679132644903083 chr18 78077248 276623447 3.542945660687221 39.31706575973582 chr19 59128983 192021731 3.247506066525785 33.781835067314724 chr20 63025520 220777131 3.502979919880074 8.699080195034947 chr21 48129895 137629903 2.859551283043522 13.386688921245948 chr22 51304566 122206541 2.3819817713690434 6.824682537657286 chrMT 16571 89329160 5390.692173073441 1191.1561681409867 chrX 155270560 279933135 1.8028732233592768 9.844319130854942 chrY 59373566 95247862 1.6042132621779868 25.864620153529756