BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472408.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 = 18,514,242 number of mapped reads = 18,348,186 (99.1%) number of supplementary alignments = 74,210 (0.4%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,204,513 number of mapped paired reads (second in pair) = 9,143,673 number of mapped paired reads (both in pair) = 18,247,380 number of mapped paired reads (singletons) = 100,806 number of mapped bases = 1,796,165,808 bp number of sequenced bases = 1,795,954,045 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,847,615 duplication rate = 47.66% >>>>>>> Insert size mean insert size = 18,656.4585 std insert size = 1,351,202.5058 median insert size = 204 >>>>>>> Mapping quality mean mapping quality = 55.2248 >>>>>>> ACTG content number of A's = 474,737,670 bp (26.43%) number of C's = 424,418,909 bp (23.63%) number of T's = 474,748,689 bp (26.43%) number of G's = 421,823,504 bp (23.49%) number of N's = 225,273 bp (0.01%) GC percentage = 47.12% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 9,628,273 number of insertions = 103,600 mapped reads with insertion percentage = 0.56% number of deletions = 84,269 mapped reads with deletion percentage = 0.45% homopolymer indels = 45.56% >>>>>>> Coverage mean coverageData = 0.5802X std coverageData = 20.056X There is a 4.99% of reference with a coverageData >= 1X There is a 2.29% of reference with a coverageData >= 2X There is a 0.96% of reference with a coverageData >= 3X There is a 0.7% of reference with a coverageData >= 4X There is a 0.5% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.4% 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 0.27% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.26% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.25% 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 0.23% 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 0.22% 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 0.21% 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 0.2% of reference with a coverageData >= 38X There is a 0.2% 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 0.19% of reference with a coverageData >= 42X There is a 0.19% 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 0.18% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.18% 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 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 241568544 0.9691793064780369 26.87517664522913 chr2 243199373 71297161 0.29316342439747983 10.171793473926327 chr3 198022430 139046053 0.7021732487577291 23.859045864232098 chr4 191154276 75409932 0.39449775112537894 16.206139245995818 chr5 180915260 120977683 0.6686980578642178 36.52070318070132 chr6 171115067 140284010 0.8198226635413701 22.027319022705143 chr7 159138663 122220637 0.7680134713711902 23.974884278685206 chr8 146364022 76323073 0.5214606155056329 13.782314121331936 chr9 141213431 85340874 0.6043396396196903 16.039280400693986 chr10 135534747 47356093 0.3494018622397989 12.139958822400246 chr11 135006516 62262705 0.4611829624579009 15.95520694636082 chr12 133851895 98747804 0.7377393050729689 20.599894363737025 chr13 115169878 28282980 0.24557619137184464 9.135174461280577 chr14 107349540 57175745 0.53261285516454 17.03356735630862 chr15 102531392 45957595 0.44822950418931207 14.061291409693492 chr16 90354753 94874753 1.050025038527857 25.927913515380887 chr17 81195210 82455315 1.0155194499774063 22.80890209123166 chr18 78077248 18912048 0.242222266850389 6.6515051767820985 chr19 59128983 43312863 0.732514932651556 15.054150053156835 chr20 63025520 34765963 0.5516172337808558 15.250742656576348 chr21 48129895 18646259 0.3874153267942928 22.62685627205781 chr22 51304566 25900394 0.5048360412989362 14.398170353673098 chrMT 16571 3811 0.22998008569187134 0.6725093132307761 chrX 155270560 62699773 0.4038097949798081 18.80030943556203 chrY 59373566 2343740 0.03947446916023201 1.683161052318989