BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618587.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 = 62,003,888 number of mapped reads = 59,606,595 (96.13%) number of supplementary alignments = 189,630 (0.31%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 30,152,736 number of mapped paired reads (second in pair) = 29,453,859 number of mapped paired reads (both in pair) = 58,350,568 number of mapped paired reads (singletons) = 1,256,027 number of mapped bases = 5,604,260,396 bp number of sequenced bases = 5,600,377,380 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,460,183 duplication rate = 25.86% >>>>>>> Insert size mean insert size = 62,567.9855 std insert size = 2,484,377.3275 median insert size = 194 >>>>>>> Mapping quality mean mapping quality = 51.6861 >>>>>>> ACTG content number of A's = 1,533,146,125 bp (27.38%) number of C's = 1,215,316,127 bp (21.7%) number of T's = 1,556,225,396 bp (27.79%) number of G's = 1,295,179,594 bp (23.13%) number of N's = 510,138 bp (0.01%) GC percentage = 44.83% >>>>>>> Mismatches and indels general error rate = 0.0133 number of mismatches = 72,697,969 number of insertions = 1,054,158 mapped reads with insertion percentage = 1.73% number of deletions = 2,825,976 mapped reads with deletion percentage = 4.62% homopolymer indels = 52.4% >>>>>>> Coverage mean coverageData = 1.8103X std coverageData = 7.7978X There is a 27.77% of reference with a coverageData >= 1X There is a 20.32% of reference with a coverageData >= 2X There is a 15.84% of reference with a coverageData >= 3X There is a 12.94% of reference with a coverageData >= 4X There is a 10.77% of reference with a coverageData >= 5X There is a 9.15% of reference with a coverageData >= 6X There is a 7.86% of reference with a coverageData >= 7X There is a 6.83% of reference with a coverageData >= 8X There is a 5.98% of reference with a coverageData >= 9X There is a 5.27% of reference with a coverageData >= 10X There is a 4.68% of reference with a coverageData >= 11X There is a 4.17% of reference with a coverageData >= 12X There is a 3.74% of reference with a coverageData >= 13X There is a 3.36% of reference with a coverageData >= 14X There is a 3.03% of reference with a coverageData >= 15X There is a 2.75% of reference with a coverageData >= 16X There is a 2.5% of reference with a coverageData >= 17X There is a 2.27% of reference with a coverageData >= 18X There is a 2.08% of reference with a coverageData >= 19X There is a 1.9% of reference with a coverageData >= 20X There is a 1.74% of reference with a coverageData >= 21X There is a 1.6% of reference with a coverageData >= 22X There is a 1.47% of reference with a coverageData >= 23X There is a 1.36% of reference with a coverageData >= 24X There is a 1.25% of reference with a coverageData >= 25X There is a 1.16% of reference with a coverageData >= 26X There is a 1.07% of reference with a coverageData >= 27X There is a 0.99% of reference with a coverageData >= 28X There is a 0.92% of reference with a coverageData >= 29X There is a 0.86% of reference with a coverageData >= 30X There is a 0.8% of reference with a coverageData >= 31X There is a 0.74% of reference with a coverageData >= 32X There is a 0.69% of reference with a coverageData >= 33X There is a 0.65% of reference with a coverageData >= 34X There is a 0.6% of reference with a coverageData >= 35X There is a 0.57% of reference with a coverageData >= 36X There is a 0.53% of reference with a coverageData >= 37X There is a 0.5% of reference with a coverageData >= 38X There is a 0.46% of reference with a coverageData >= 39X There is a 0.44% of reference with a coverageData >= 40X There is a 0.41% of reference with a coverageData >= 41X There is a 0.38% of reference with a coverageData >= 42X There is a 0.36% of reference with a coverageData >= 43X There is a 0.34% of reference with a coverageData >= 44X There is a 0.32% of reference with a coverageData >= 45X There is a 0.3% of reference with a coverageData >= 46X There is a 0.28% of reference with a coverageData >= 47X There is a 0.27% of reference with a coverageData >= 48X There is a 0.25% of reference with a coverageData >= 49X There is a 0.24% of reference with a coverageData >= 50X There is a 0.23% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 507317925 2.0353727624213223 8.953855169759521 chr2 243199373 487708716 2.0053864036894535 10.138342053680427 chr3 198022430 375090657 1.8941826792045728 5.748521089005614 chr4 191154276 298954966 1.563946003488826 5.893272855061792 chr5 180915260 335271589 1.8531968447548317 5.85964029168347 chr6 171115067 316435973 1.8492583882166262 6.36401914199033 chr7 159138663 294056595 1.8478010902982136 5.950269760788844 chr8 146364022 287220997 1.9623743121789863 6.120818151016143 chr9 141213431 250006584 1.7704164698044904 7.63732895664408 chr10 135534747 296217947 2.1855498575579295 6.873931447282963 chr11 135006516 291783761 2.161256875927381 7.438724767060839 chr12 133851895 263089472 1.9655266890319334 7.75852017092487 chr13 115169878 155838695 1.3531202577118298 4.733046187415436 chr14 107349540 173770804 1.6187382265447994 5.5389348994995276 chr15 102531392 192478694 1.8772659791842092 6.359056521091522 chr16 90354753 210282988 2.327304109834709 20.519443705090875 chr17 81195210 188428084 2.320679803648516 7.704881165872391 chr18 78077248 143317380 1.8355844201885805 7.344625076105312 chr19 59128983 124906826 2.112446716697292 7.766465221157355 chr20 63025520 169449352 2.688583164407053 7.762857274579247 chr21 48129895 78052964 1.6217148198640368 8.934725133325191 chr22 51304566 101497956 1.9783415768491248 7.145445856329189 chrMT 16571 6243 0.37674250196125764 1.5928131518370956 chrX 155270560 9535199 0.06141021839555419 1.6613886414312327 chrY 59373566 53540029 0.901748582862616 7.7473748581444095