BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777264.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 3,955,548 number of mapped reads = 3,788,672 (95.78%) number of supplementary alignments = 73,202 (1.85%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,901,387 number of mapped paired reads (second in pair) = 1,887,285 number of mapped paired reads (both in pair) = 3,763,538 number of mapped paired reads (singletons) = 25,134 number of mapped bases = 282,722,876 bp number of sequenced bases = 282,671,250 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 79,038 duplication rate = 1.95% >>>>>>> Insert size mean insert size = 169,483.9569 std insert size = 4,001,265.1189 median insert size = 157 >>>>>>> Mapping quality mean mapping quality = 52.606 >>>>>>> ACTG content number of A's = 84,140,257 bp (29.77%) number of C's = 57,617,835 bp (20.38%) number of T's = 82,368,758 bp (29.14%) number of G's = 58,527,844 bp (20.71%) number of N's = 16,556 bp (0.01%) GC percentage = 41.09% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 1,530,885 number of insertions = 55,535 mapped reads with insertion percentage = 1.45% number of deletions = 26,083 mapped reads with deletion percentage = 0.68% homopolymer indels = 49.45% >>>>>>> Coverage mean coverageData = 0.0913X std coverageData = 0.404X There is a 7.46% of reference with a coverageData >= 1X There is a 1.4% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 23917728 0.09595854928682404 0.4679727160133129 chr2 243199373 26976628 0.11092392084415448 0.39910452534035007 chr3 198022430 19195871 0.09693786203916395 0.35568138689822637 chr4 191154276 17629979 0.09222905900362909 0.349591232462202 chr5 180915260 19465907 0.10759682184908007 0.37495584971791873 chr6 171115067 13518651 0.0790032767833355 0.3566686599522841 chr7 159138663 19071163 0.11983990967675781 0.42557503349317294 chr8 146364022 14131321 0.09654914375064112 0.36389544081323894 chr9 141213431 10437326 0.0739117088657098 0.42253065967717013 chr10 135534747 12841482 0.09474678843794943 0.42111933805008767 chr11 135006516 15732058 0.11652813853814285 0.407514612834466 chr12 133851895 13008432 0.0971852658492433 0.3552810631229985 chr13 115169878 12157218 0.10555900736475557 0.3733013936383283 chr14 107349540 5775116 0.05379730551244095 0.2641069398992934 chr15 102531392 10595013 0.10333433296214295 0.37039777132614116 chr16 90354753 7381352 0.08169301287337923 0.34941567094572945 chr17 81195210 6789234 0.0836161886889633 0.3571534088303729 chr18 78077248 6181256 0.07916846659349469 0.4304787945996422 chr19 59128983 3488074 0.0589909351222902 0.35540276180392383 chr20 63025520 7439513 0.11803969249281879 0.39350842937612934 chr21 48129895 2577039 0.05354341620732811 0.2775730726795757 chr22 51304566 2126633 0.04145114491369053 0.23281117596574907 chrMT 16571 1001949 60.464003379397745 16.24948516352457 chrX 155270560 10935981 0.07043177405942247 0.307682164861927 chrY 59373566 347952 0.005860385748095373 0.15505998916883904