BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618570.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 216,922,566 number of mapped reads = 210,412,403 (97%) number of supplementary alignments = 2,212,451 (1.02%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 105,602,901 number of mapped paired reads (second in pair) = 104,809,502 number of mapped paired reads (both in pair) = 208,080,656 number of mapped paired reads (singletons) = 2,331,747 number of mapped bases = 19,880,980,065 bp number of sequenced bases = 19,867,398,173 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 81,121,881 duplication rate = 31.54% >>>>>>> Insert size mean insert size = 122,946.3803 std insert size = 3,488,036.5376 median insert size = 185 >>>>>>> Mapping quality mean mapping quality = 52.3888 >>>>>>> ACTG content number of A's = 5,263,947,989 bp (26.5%) number of C's = 4,480,365,979 bp (22.55%) number of T's = 5,312,462,377 bp (26.74%) number of G's = 4,808,665,717 bp (24.2%) number of N's = 1,956,111 bp (0.01%) GC percentage = 46.76% >>>>>>> Mismatches and indels general error rate = 0.0131 number of mismatches = 255,281,034 number of insertions = 3,336,007 mapped reads with insertion percentage = 1.56% number of deletions = 9,795,690 mapped reads with deletion percentage = 4.54% homopolymer indels = 52.03% >>>>>>> Coverage mean coverageData = 6.4221X std coverageData = 24.5232X There is a 41.71% of reference with a coverageData >= 1X There is a 34.03% of reference with a coverageData >= 2X There is a 29.04% of reference with a coverageData >= 3X There is a 25.57% of reference with a coverageData >= 4X There is a 22.84% of reference with a coverageData >= 5X There is a 20.68% of reference with a coverageData >= 6X There is a 18.87% of reference with a coverageData >= 7X There is a 17.35% of reference with a coverageData >= 8X There is a 16.05% of reference with a coverageData >= 9X There is a 14.91% of reference with a coverageData >= 10X There is a 13.91% of reference with a coverageData >= 11X There is a 13.02% of reference with a coverageData >= 12X There is a 12.23% of reference with a coverageData >= 13X There is a 11.52% of reference with a coverageData >= 14X There is a 10.87% of reference with a coverageData >= 15X There is a 10.29% of reference with a coverageData >= 16X There is a 9.75% of reference with a coverageData >= 17X There is a 9.26% of reference with a coverageData >= 18X There is a 8.8% of reference with a coverageData >= 19X There is a 8.39% of reference with a coverageData >= 20X There is a 8% of reference with a coverageData >= 21X There is a 7.64% of reference with a coverageData >= 22X There is a 7.3% of reference with a coverageData >= 23X There is a 6.99% of reference with a coverageData >= 24X There is a 6.7% of reference with a coverageData >= 25X There is a 6.43% of reference with a coverageData >= 26X There is a 6.17% of reference with a coverageData >= 27X There is a 5.93% of reference with a coverageData >= 28X There is a 5.7% of reference with a coverageData >= 29X There is a 5.49% of reference with a coverageData >= 30X There is a 5.29% of reference with a coverageData >= 31X There is a 5.1% of reference with a coverageData >= 32X There is a 4.92% of reference with a coverageData >= 33X There is a 4.75% of reference with a coverageData >= 34X There is a 4.58% of reference with a coverageData >= 35X There is a 4.43% of reference with a coverageData >= 36X There is a 4.28% of reference with a coverageData >= 37X There is a 4.14% of reference with a coverageData >= 38X There is a 4.01% of reference with a coverageData >= 39X There is a 3.88% of reference with a coverageData >= 40X There is a 3.76% of reference with a coverageData >= 41X There is a 3.64% of reference with a coverageData >= 42X There is a 3.53% of reference with a coverageData >= 43X There is a 3.42% of reference with a coverageData >= 44X There is a 3.32% of reference with a coverageData >= 45X There is a 3.23% of reference with a coverageData >= 46X There is a 3.13% of reference with a coverageData >= 47X There is a 3.04% of reference with a coverageData >= 48X There is a 2.96% of reference with a coverageData >= 49X There is a 2.87% of reference with a coverageData >= 50X There is a 2.79% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1813283054 7.274938961937431 29.252349559831885 chr2 243199373 1724282991 7.089997682683171 28.250103581206954 chr3 198022430 1333751466 6.7353555150292825 20.619937056907666 chr4 191154276 1027294843 5.374166168273422 20.745364137134676 chr5 180915260 1172389666 6.4803249101264315 20.265067989913444 chr6 171115067 1115691729 6.520125600628727 21.090594650549264 chr7 159138663 1029068589 6.466490101151598 20.70275356237789 chr8 146364022 1024622394 7.000507228477228 21.34706828826291 chr9 141213431 884329682 6.262362409422656 26.729969238072048 chr10 135534747 1050988181 7.75438184128532 23.688364813001147 chr11 135006516 1019880997 7.554309430516672 27.379343864767428 chr12 133851895 955563483 7.138961185420647 22.505655239697898 chr13 115169878 546290148 4.743342247874917 16.847837546094045 chr14 107349540 646251234 6.020065237354534 21.480891884263787 chr15 102531392 701506912 6.84187445733693 23.681725134739263 chr16 90354753 747380380 8.271622191253181 41.13557112728999 chr17 81195210 666765491 8.211882092552012 26.919974757245573 chr18 78077248 514033269 6.583649938583901 27.83156276083986 chr19 59128983 442521876 7.484009593062002 27.8677394326039 chr20 63025520 603734395 9.579205296521156 28.65132210544011 chr21 48129895 261285573 5.428758425506642 37.168534562198836 chr22 51304566 365063647 7.115617097316446 27.763015025138245 chrMT 16571 29647 1.789089373001026 4.951820551316427 chrX 155270560 41836973 0.2694456244635171 5.191179072230586 chrY 59373566 193133445 3.2528523720471836 21.549056023475796