BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084809.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,829,147 number of mapped reads = 2,579,194 (91.17%) number of supplementary alignments = 31,424 (1.11%) number of secondary alignments = 0 number of mapped bases = 173,483,658 bp number of sequenced bases = 173,417,104 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 110,757 duplication rate = 3.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7865 >>>>>>> ACTG content number of A's = 47,732,905 bp (27.52%) number of C's = 32,635,044 bp (18.82%) number of T's = 54,281,769 bp (31.3%) number of G's = 38,742,544 bp (22.34%) number of N's = 24,842 bp (0.01%) GC percentage = 41.16% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,322,980 number of insertions = 13,740 mapped reads with insertion percentage = 0.53% number of deletions = 40,003 mapped reads with deletion percentage = 1.53% homopolymer indels = 48.18% >>>>>>> Coverage mean coverageData = 0.056X std coverageData = 0.3318X There is a 4.65% of reference with a coverageData >= 1X There is a 0.73% of reference with a coverageData >= 2X There is a 0.14% 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 0.01% 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 14071267 0.05645429063946043 0.36414107061512724 chr2 243199373 14053916 0.05778763253637171 0.5261098019123427 chr3 198022430 12668335 0.06397424271583779 0.29593932289213837 chr4 191154276 9857077 0.05156608162926996 0.2702132996204294 chr5 180915260 8843081 0.04887968543947039 0.2574864413705624 chr6 171115067 10028940 0.05860933333240608 0.30096737464224954 chr7 159138663 11293409 0.07096584065180943 0.36971679184690154 chr8 146364022 11351229 0.07755477640536552 0.3901067082008326 chr9 141213431 11512179 0.08152325822322098 0.39855815479250173 chr10 135534747 5561787 0.04103587547184487 0.2494084311084087 chr11 135006516 6680708 0.049484337481903465 0.291229470211598 chr12 133851895 8735105 0.06525947951652085 0.29959265076369224 chr13 115169878 3889289 0.03377001927535254 0.21453681121697016 chr14 107349540 3867437 0.03602658194902372 0.22154485397172977 chr15 102531392 4499018 0.04387941987562209 0.25327212392097903 chr16 90354753 3179238 0.03518617332726259 0.2235713043333152 chr17 81195210 4962740 0.0611210932270512 0.2924016171154085 chr18 78077248 6981552 0.0894185204888369 0.5266607940822022 chr19 59128983 3243276 0.05485086729802202 0.3227548882677606 chr20 63025520 3547789 0.0562913086635382 0.2785511875730557 chr21 48129895 1665474 0.03460373225414267 0.22045479811856 chr22 51304566 2072483 0.040395683300390846 0.23207878630481538 chrMT 16571 60780 3.667853478969284 2.6560775662733334 chrX 155270560 10500569 0.06762755927459783 0.31163047963998414 chrY 59373566 356980 0.006012439946760146 0.11394528971996189