BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472794.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 = 15,387,760 number of mapped reads = 15,215,885 (98.88%) number of supplementary alignments = 53,568 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,632,501 number of mapped paired reads (second in pair) = 7,583,384 number of mapped paired reads (both in pair) = 15,131,320 number of mapped paired reads (singletons) = 84,565 number of mapped bases = 1,496,637,612 bp number of sequenced bases = 1,496,446,226 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,082,852 duplication rate = 46.95% >>>>>>> Insert size mean insert size = 27,217.145 std insert size = 1,611,359.3377 median insert size = 232 >>>>>>> Mapping quality mean mapping quality = 54.7007 >>>>>>> ACTG content number of A's = 416,553,565 bp (27.84%) number of C's = 333,899,752 bp (22.31%) number of T's = 413,540,613 bp (27.63%) number of G's = 332,163,208 bp (22.2%) number of N's = 289,088 bp (0.02%) GC percentage = 44.51% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 8,912,388 number of insertions = 83,416 mapped reads with insertion percentage = 0.54% number of deletions = 81,992 mapped reads with deletion percentage = 0.53% homopolymer indels = 44.33% >>>>>>> Coverage mean coverageData = 0.4835X std coverageData = 19.8656X There is a 4.06% of reference with a coverageData >= 1X There is a 1.83% of reference with a coverageData >= 2X There is a 0.84% of reference with a coverageData >= 3X There is a 0.59% of reference with a coverageData >= 4X There is a 0.44% of reference with a coverageData >= 5X There is a 0.38% of reference with a coverageData >= 6X There is a 0.34% of reference with a coverageData >= 7X There is a 0.31% of reference with a coverageData >= 8X There is a 0.29% of reference with a coverageData >= 9X There is a 0.28% of reference with a coverageData >= 10X There is a 0.27% of reference with a coverageData >= 11X There is a 0.26% of reference with a coverageData >= 12X There is a 0.25% of reference with a coverageData >= 13X There is a 0.24% of reference with a coverageData >= 14X There is a 0.23% of reference with a coverageData >= 15X There is a 0.23% of reference with a coverageData >= 16X There is a 0.22% of reference with a coverageData >= 17X There is a 0.22% of reference with a coverageData >= 18X There is a 0.21% of reference with a coverageData >= 19X There is a 0.21% of reference with a coverageData >= 20X There is a 0.2% of reference with a coverageData >= 21X There is a 0.2% of reference with a coverageData >= 22X There is a 0.19% of reference with a coverageData >= 23X There is a 0.19% of reference with a coverageData >= 24X There is a 0.19% of reference with a coverageData >= 25X There is a 0.18% of reference with a coverageData >= 26X There is a 0.18% of reference with a coverageData >= 27X There is a 0.18% of reference with a coverageData >= 28X There is a 0.17% of reference with a coverageData >= 29X There is a 0.17% of reference with a coverageData >= 30X There is a 0.17% of reference with a coverageData >= 31X There is a 0.16% of reference with a coverageData >= 32X There is a 0.16% of reference with a coverageData >= 33X There is a 0.16% of reference with a coverageData >= 34X There is a 0.16% of reference with a coverageData >= 35X There is a 0.15% of reference with a coverageData >= 36X There is a 0.15% of reference with a coverageData >= 37X There is a 0.15% of reference with a coverageData >= 38X There is a 0.15% of reference with a coverageData >= 39X There is a 0.15% of reference with a coverageData >= 40X There is a 0.14% of reference with a coverageData >= 41X There is a 0.14% of reference with a coverageData >= 42X There is a 0.14% of reference with a coverageData >= 43X There is a 0.14% of reference with a coverageData >= 44X There is a 0.14% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.13% of reference with a coverageData >= 47X There is a 0.13% of reference with a coverageData >= 48X There is a 0.13% of reference with a coverageData >= 49X There is a 0.13% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 133321934 0.5348910805722726 20.32247420334548 chr2 243199373 122805147 0.5049566760190619 26.198702157328977 chr3 198022430 231881409 1.1709855747149451 32.910429794596816 chr4 191154276 37662123 0.19702474769646272 9.6158647469549 chr5 180915260 69529124 0.38431873574401626 14.230006196801385 chr6 171115067 163844260 0.9575092531156242 31.98099795925339 chr7 159138663 28163466 0.176974378627273 6.124316609259999 chr8 146364022 90801542 0.6203815716406044 28.011413104691755 chr9 141213431 134402794 0.9517706145104569 29.529534797591364 chr10 135534747 43337913 0.3197549998008998 13.478777547032072 chr11 135006516 68628733 0.5083364494792236 20.744757030624005 chr12 133851895 65853321 0.4919864675804552 16.55246869320547 chr13 115169878 14540654 0.12625396720486237 5.726845051802156 chr14 107349540 52436213 0.4884623911755933 17.19179851088097 chr15 102531392 27854348 0.2716665350646951 12.949844568715813 chr16 90354753 19680725 0.2178161562790172 7.222093797762953 chr17 81195210 43571633 0.536628121289421 14.967190992534018 chr18 78077248 20033206 0.25658186620512036 12.141566727860276 chr19 59128983 19130778 0.32354315987474364 8.688957222620132 chr20 63025520 33700577 0.5347131923703288 18.17746376277227 chr21 48129895 9788483 0.2033763630691486 8.666548561683735 chr22 51304566 7763508 0.15132197005623244 11.504136189476643 chrMT 16571 6810 0.410958904109589 1.2465833002058395 chrX 155270560 54792868 0.35288639391781673 11.476005707141093 chrY 59373566 3106043 0.05231356661312881 4.427434809555458