BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618664.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 = 479,430,622 number of mapped reads = 460,831,302 (96.12%) number of supplementary alignments = 892,547 (0.19%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 230,748,310 number of mapped paired reads (second in pair) = 230,082,992 number of mapped paired reads (both in pair) = 453,433,662 number of mapped paired reads (singletons) = 7,397,640 number of mapped bases = 44,607,406,580 bp number of sequenced bases = 44,594,154,672 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 134,526,566 duplication rate = 22.65% >>>>>>> Insert size mean insert size = 29,692.9041 std insert size = 1,633,788.46 median insert size = 238 >>>>>>> Mapping quality mean mapping quality = 53.6504 >>>>>>> ACTG content number of A's = 13,252,624,228 bp (29.72%) number of C's = 9,094,167,280 bp (20.39%) number of T's = 13,197,762,925 bp (29.6%) number of G's = 9,046,283,899 bp (20.29%) number of N's = 3,316,340 bp (0.01%) GC percentage = 40.68% >>>>>>> Mismatches and indels general error rate = 0.0117 number of mismatches = 507,753,503 number of insertions = 5,174,636 mapped reads with insertion percentage = 1.09% number of deletions = 5,726,247 mapped reads with deletion percentage = 1.21% homopolymer indels = 40.83% >>>>>>> Coverage mean coverageData = 14.4095X std coverageData = 156.2724X There is a 92.14% of reference with a coverageData >= 1X There is a 91.89% of reference with a coverageData >= 2X There is a 91.47% of reference with a coverageData >= 3X There is a 90.76% of reference with a coverageData >= 4X There is a 89.66% of reference with a coverageData >= 5X There is a 88.08% of reference with a coverageData >= 6X There is a 85.89% of reference with a coverageData >= 7X There is a 83.01% of reference with a coverageData >= 8X There is a 79.38% of reference with a coverageData >= 9X There is a 74.97% of reference with a coverageData >= 10X There is a 69.84% of reference with a coverageData >= 11X There is a 64.1% of reference with a coverageData >= 12X There is a 57.91% of reference with a coverageData >= 13X There is a 51.48% of reference with a coverageData >= 14X There is a 45.02% of reference with a coverageData >= 15X There is a 38.74% of reference with a coverageData >= 16X There is a 32.82% of reference with a coverageData >= 17X There is a 27.38% of reference with a coverageData >= 18X There is a 22.52% of reference with a coverageData >= 19X There is a 18.27% of reference with a coverageData >= 20X There is a 14.65% of reference with a coverageData >= 21X There is a 11.61% of reference with a coverageData >= 22X There is a 9.11% of reference with a coverageData >= 23X There is a 7.09% of reference with a coverageData >= 24X There is a 5.49% of reference with a coverageData >= 25X There is a 4.23% of reference with a coverageData >= 26X There is a 3.25% of reference with a coverageData >= 27X There is a 2.51% of reference with a coverageData >= 28X There is a 1.94% of reference with a coverageData >= 29X There is a 1.52% of reference with a coverageData >= 30X There is a 1.2% of reference with a coverageData >= 31X There is a 0.96% of reference with a coverageData >= 32X There is a 0.79% of reference with a coverageData >= 33X There is a 0.66% of reference with a coverageData >= 34X There is a 0.56% of reference with a coverageData >= 35X There is a 0.49% of reference with a coverageData >= 36X There is a 0.44% of reference with a coverageData >= 37X There is a 0.39% of reference with a coverageData >= 38X There is a 0.36% of reference with a coverageData >= 39X There is a 0.33% of reference with a coverageData >= 40X There is a 0.31% of reference with a coverageData >= 41X There is a 0.3% of reference with a coverageData >= 42X There is a 0.28% of reference with a coverageData >= 43X There is a 0.27% of reference with a coverageData >= 44X There is a 0.26% of reference with a coverageData >= 45X There is a 0.25% of reference with a coverageData >= 46X There is a 0.24% of reference with a coverageData >= 47X There is a 0.23% of reference with a coverageData >= 48X There is a 0.22% of reference with a coverageData >= 49X There is a 0.21% of reference with a coverageData >= 50X There is a 0.21% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3653201242 14.656738776991853 367.23658727222954 chr2 243199373 3859958796 15.871582020896081 88.29477875587128 chr3 198022430 2999566318 15.147608874408823 9.24732527727745 chr4 191154276 3068937597 16.054768228150962 136.1833256657275 chr5 180915260 2734455148 15.114563293334127 11.66178918683885 chr6 171115067 2615212550 15.283356374456494 70.49943350573506 chr7 159138663 2430270440 15.271401645494533 111.39889358264672 chr8 146364022 2301853209 15.726905953704934 221.62536813672597 chr9 141213431 1912130952 13.540715911080724 160.149778861402 chr10 135534747 2360082310 17.413116283752682 318.5360148239785 chr11 135006516 2058688280 15.248806805739658 75.02032987011269 chr12 133851895 1992454104 14.885512857326376 11.937970941737115 chr13 115169878 1458797313 12.666483097255691 8.62271228660926 chr14 107349540 1358947356 12.659088767404127 12.906258073331255 chr15 102531392 1270682135 12.393103323906887 8.950917681983208 chr16 90354753 1371710244 15.181384470167275 105.8932728469321 chr17 81195210 1190474039 14.661875238699425 70.58321861351924 chr18 78077248 1277900774 16.367133918449586 207.74636120083346 chr19 59128983 833295661 14.092846159725088 148.87295130213448 chr20 63025520 920207145 14.600548238237463 39.44263184845374 chr21 48129895 624550984 12.976362902931744 60.15749476462867 chr22 51304566 534600469 10.420134320988117 59.83346828544027 chrMT 16571 22651748 1366.9511797718906 176.5756405485342 chrX 155270560 1219624014 7.854831038156879 28.46562685116784 chrY 59373566 537153752 9.04701853346656 162.95440568499941