BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472515.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 16,748,238 number of mapped reads = 16,549,842 (98.82%) number of supplementary alignments = 68,337 (0.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,302,851 number of mapped paired reads (second in pair) = 8,246,991 number of mapped paired reads (both in pair) = 16,445,410 number of mapped paired reads (singletons) = 104,432 number of mapped bases = 1,625,560,480 bp number of sequenced bases = 1,625,370,241 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,165,100 duplication rate = 46.29% >>>>>>> Insert size mean insert size = 29,699.009 std insert size = 1,663,090.0537 median insert size = 232 >>>>>>> Mapping quality mean mapping quality = 55.1977 >>>>>>> ACTG content number of A's = 450,669,184 bp (27.73%) number of C's = 364,790,436 bp (22.44%) number of T's = 448,200,848 bp (27.58%) number of G's = 361,457,294 bp (22.24%) number of N's = 252,479 bp (0.02%) GC percentage = 44.68% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 9,799,475 number of insertions = 86,392 mapped reads with insertion percentage = 0.52% number of deletions = 78,737 mapped reads with deletion percentage = 0.47% homopolymer indels = 45.24% >>>>>>> Coverage mean coverageData = 0.5251X std coverageData = 17.0968X There is a 5.25% of reference with a coverageData >= 1X There is a 2.33% of reference with a coverageData >= 2X There is a 0.98% of reference with a coverageData >= 3X There is a 0.7% of reference with a coverageData >= 4X There is a 0.51% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.41% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.35% of reference with a coverageData >= 10X There is a 0.34% of reference with a coverageData >= 11X There is a 0.33% of reference with a coverageData >= 12X There is a 0.32% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.3% of reference with a coverageData >= 15X There is a 0.29% of reference with a coverageData >= 16X There is a 0.28% of reference with a coverageData >= 17X There is a 0.28% of reference with a coverageData >= 18X There is a 0.27% of reference with a coverageData >= 19X There is a 0.26% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.25% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.24% of reference with a coverageData >= 25X There is a 0.24% of reference with a coverageData >= 26X There is a 0.23% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.22% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.2% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.19% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 175017796 0.7021759676979902 24.086254805872056 chr2 243199373 118248155 0.4862189961320336 15.259275480130503 chr3 198022430 186217200 0.9403843796887049 19.536009170645972 chr4 191154276 75947160 0.3973081930952986 16.058524613774853 chr5 180915260 80168163 0.4431254886956468 13.410281044674559 chr6 171115067 98534589 0.5758381814501466 16.090396129023826 chr7 159138663 66192008 0.4159391988859426 12.496553185724913 chr8 146364022 82965912 0.5668463524458217 20.9207614289856 chr9 141213431 94990789 0.6726753137242306 16.076676329816586 chr10 135534747 34960236 0.2579429760546939 7.7382682295232526 chr11 135006516 61192223 0.45325384887348696 13.016932593223116 chr12 133851895 79294558 0.592405195309338 20.70898938456193 chr13 115169878 27470886 0.23852492055257712 8.006545439016593 chr14 107349540 32935423 0.30680544136472315 10.708063608205531 chr15 102531392 42300990 0.4125662314230553 13.444840743886056 chr16 90354753 51001751 0.5644611855670725 17.142569122793805 chr17 81195210 58956312 0.7261057887528094 17.00909519663488 chr18 78077248 38678244 0.495384314775029 17.11571903878749 chr19 59128983 35885783 0.6069068192835314 18.165440817042224 chr20 63025520 48088736 0.7630041925873836 24.072544562394356 chr21 48129895 9161462 0.1903486803783802 7.737318581707955 chr22 51304566 18399013 0.35862330460021824 12.718656078509557 chrMT 16571 945 0.0570273369138857 0.3086965093538238 chrX 155270560 104227746 0.6712653448277639 26.472863174965774 chrY 59373566 4724400 0.07957076386484854 3.772616496228887