BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084862.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 = 1,972,464 number of mapped reads = 1,691,356 (85.75%) number of supplementary alignments = 11,255 (0.57%) number of secondary alignments = 0 number of mapped bases = 117,006,938 bp number of sequenced bases = 116,957,866 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 73,590 duplication rate = 2.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6101 >>>>>>> ACTG content number of A's = 34,130,872 bp (29.18%) number of C's = 21,547,670 bp (18.42%) number of T's = 36,790,707 bp (31.46%) number of G's = 24,470,284 bp (20.92%) number of N's = 18,333 bp (0.02%) GC percentage = 39.35% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 1,086,547 number of insertions = 10,197 mapped reads with insertion percentage = 0.6% number of deletions = 27,819 mapped reads with deletion percentage = 1.63% homopolymer indels = 47.14% >>>>>>> Coverage mean coverageData = 0.0378X std coverageData = 0.5044X There is a 3.35% of reference with a coverageData >= 1X There is a 0.29% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 10732475 0.04305896995137276 1.1921449366781482 chr2 243199373 10111955 0.04157886953104933 0.511466376424763 chr3 198022430 8129583 0.041053849303838964 0.22159894607046715 chr4 191154276 7602662 0.039772387827725075 0.22392337651047886 chr5 180915260 6374623 0.03523540800261957 0.22485494902215356 chr6 171115067 7103191 0.04151119550448471 0.23709130007639567 chr7 159138663 6931165 0.04355424929013008 0.4293149087102132 chr8 146364022 7360889 0.05029165569117799 0.8627977007805846 chr9 141213431 6601922 0.046751374520459035 0.4245171955855441 chr10 135534747 4744130 0.0350030534974179 0.37198604178301375 chr11 135006516 4636369 0.034341816509063906 0.35837603377084193 chr12 133851895 4880879 0.03646477324807393 0.2174704222041926 chr13 115169878 3481485 0.030229128140606347 0.1858390120509475 chr14 107349540 2122544 0.019772269168549766 0.1911100794380775 chr15 102531392 2814290 0.027448081461724425 0.18033574900085114 chr16 90354753 2060725 0.02280704591157479 0.22772888910679065 chr17 81195210 2916434 0.035918793731797724 0.23894910101845815 chr18 78077248 4187888 0.05363775116663948 0.8848320035875645 chr19 59128983 2538414 0.04293011432312306 0.6370526467236761 chr20 63025520 1998335 0.031706759420628346 0.22772717045766097 chr21 48129895 1304078 0.02709496872993386 0.19585808291387866 chr22 51304566 1219748 0.02377464804984414 0.16476772073485899 chrMT 16571 12107 0.7306137227686923 0.9332428058403331 chrX 155270560 6867765 0.04423095401987344 0.2828488722052442 chrY 59373566 273282 0.004602755374336114 0.11155115428333663