BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975230.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 108,769,624 number of mapped reads = 108,568,566 (99.82%) number of supplementary alignments = 1,539,095 (1.42%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 54,290,998 number of mapped paired reads (second in pair) = 54,277,568 number of mapped paired reads (both in pair) = 108,517,714 number of mapped paired reads (singletons) = 50,852 number of mapped bases = 10,573,251,039 bp number of sequenced bases = 10,571,951,797 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 72,010,793 duplication rate = 54.91% >>>>>>> Insert size mean insert size = 87,633.2301 std insert size = 2,981,911.7407 median insert size = 142 >>>>>>> Mapping quality mean mapping quality = 56.0348 >>>>>>> ACTG content number of A's = 2,354,051,671 bp (22.27%) number of C's = 2,922,888,381 bp (27.65%) number of T's = 2,419,581,884 bp (22.89%) number of G's = 2,875,022,998 bp (27.19%) number of N's = 406,863 bp (0%) GC percentage = 54.84% >>>>>>> Mismatches and indels general error rate = 0.0029 number of mismatches = 29,930,983 number of insertions = 615,136 mapped reads with insertion percentage = 0.56% number of deletions = 566,847 mapped reads with deletion percentage = 0.51% homopolymer indels = 34.49% >>>>>>> Coverage mean coverageData = 3.4155X std coverageData = 39.4131X There is a 11.22% of reference with a coverageData >= 1X There is a 6.97% of reference with a coverageData >= 2X There is a 4.47% of reference with a coverageData >= 3X There is a 3.72% of reference with a coverageData >= 4X There is a 3.14% of reference with a coverageData >= 5X There is a 2.89% of reference with a coverageData >= 6X There is a 2.68% of reference with a coverageData >= 7X There is a 2.56% of reference with a coverageData >= 8X There is a 2.46% of reference with a coverageData >= 9X There is a 2.39% of reference with a coverageData >= 10X There is a 2.33% of reference with a coverageData >= 11X There is a 2.27% of reference with a coverageData >= 12X There is a 2.22% of reference with a coverageData >= 13X There is a 2.18% of reference with a coverageData >= 14X There is a 2.14% of reference with a coverageData >= 15X There is a 2.1% of reference with a coverageData >= 16X There is a 2.07% of reference with a coverageData >= 17X There is a 2.03% of reference with a coverageData >= 18X There is a 2% of reference with a coverageData >= 19X There is a 1.97% of reference with a coverageData >= 20X There is a 1.94% of reference with a coverageData >= 21X There is a 1.91% of reference with a coverageData >= 22X There is a 1.89% of reference with a coverageData >= 23X There is a 1.86% of reference with a coverageData >= 24X There is a 1.84% of reference with a coverageData >= 25X There is a 1.81% of reference with a coverageData >= 26X There is a 1.79% of reference with a coverageData >= 27X There is a 1.77% of reference with a coverageData >= 28X There is a 1.74% of reference with a coverageData >= 29X There is a 1.72% of reference with a coverageData >= 30X There is a 1.7% of reference with a coverageData >= 31X There is a 1.68% of reference with a coverageData >= 32X There is a 1.66% of reference with a coverageData >= 33X There is a 1.64% of reference with a coverageData >= 34X There is a 1.62% of reference with a coverageData >= 35X There is a 1.6% of reference with a coverageData >= 36X There is a 1.58% of reference with a coverageData >= 37X There is a 1.57% of reference with a coverageData >= 38X There is a 1.55% of reference with a coverageData >= 39X There is a 1.53% of reference with a coverageData >= 40X There is a 1.51% of reference with a coverageData >= 41X There is a 1.5% of reference with a coverageData >= 42X There is a 1.48% of reference with a coverageData >= 43X There is a 1.47% of reference with a coverageData >= 44X There is a 1.45% of reference with a coverageData >= 45X There is a 1.44% of reference with a coverageData >= 46X There is a 1.42% of reference with a coverageData >= 47X There is a 1.41% of reference with a coverageData >= 48X There is a 1.39% of reference with a coverageData >= 49X There is a 1.38% of reference with a coverageData >= 50X There is a 1.36% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1237847395 4.966276071986195 49.636987226494924 chr2 243199373 703686457 2.8934550624848856 33.148705429418285 chr3 198022430 545390481 2.754185376878771 30.424000554536416 chr4 191154276 305998302 1.600792346387271 22.048579038076284 chr5 180915260 455693867 2.518824929417231 31.03951057870068 chr6 171115067 516226093 3.0168359925897117 34.83378249054793 chr7 159138663 512561984 3.2208513904631713 35.7300093668768 chr8 146364022 363790062 2.485515613939606 31.75548059481166 chr9 141213431 407290248 2.884217493447914 32.35271015778482 chr10 135534747 358329851 2.6438227755720827 30.67540347121878 chr11 135006516 700799116 5.190854017742374 48.08114341603253 chr12 133851895 544498523 4.06791792525612 40.97483209475948 chr13 115169878 119684207 1.039197132778069 15.81515064237084 chr14 107349540 334128991 3.112533048581298 35.13252644187126 chr15 102531392 264616058 2.58082966434319 26.70256511704306 chr16 90354753 501235902 5.5474215285608715 50.10517458450615 chr17 81195210 789730451 9.726318227392971 70.55615564645986 chr18 78077248 147133093 1.884455417793414 26.8933604678323 chr19 59128983 933193904 15.782343220751827 104.97566207887486 chr20 63025520 259771318 4.121684644569374 39.79417516333449 chr21 48129895 133459266 2.772897509957169 78.56817281039822 chr22 51304566 221582944 4.318971219832559 37.43753827810501 chrMT 16571 701376 42.325508418321164 52.63056633869513 chrX 155270560 204638166 1.317945694277138 17.0871457209479 chrY 59373566 11262984 0.18969694358597225 4.809195909383112