BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080918.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 = 3,043,294 number of mapped reads = 2,730,775 (89.73%) number of supplementary alignments = 31,683 (1.04%) number of secondary alignments = 0 number of mapped bases = 187,986,666 bp number of sequenced bases = 187,918,463 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 104,448 duplication rate = 3.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.8006 >>>>>>> ACTG content number of A's = 54,306,890 bp (28.9%) number of C's = 33,416,891 bp (17.78%) number of T's = 60,016,632 bp (31.94%) number of G's = 39,272,714 bp (20.9%) number of N's = 905,336 bp (0.48%) GC percentage = 38.68% >>>>>>> Mismatches and indels general error rate = 0.0114 number of mismatches = 2,115,728 number of insertions = 14,083 mapped reads with insertion percentage = 0.51% number of deletions = 41,556 mapped reads with deletion percentage = 1.5% homopolymer indels = 49.84% >>>>>>> Coverage mean coverageData = 0.0607X std coverageData = 0.4252X There is a 4.75% of reference with a coverageData >= 1X There is a 0.97% of reference with a coverageData >= 2X There is a 0.22% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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 15607276 0.06261679885644096 0.600406896277516 chr2 243199373 16909716 0.06953026149454752 0.41251316819699435 chr3 198022430 12857298 0.06492849320150247 0.3111606099496487 chr4 191154276 14514130 0.07592887956113521 0.34607762956152965 chr5 180915260 11120230 0.06146651200125407 0.3044195929328775 chr6 171115067 12274639 0.07173324485797618 0.3994454287225433 chr7 159138663 10191583 0.06404215548800984 0.5484911184615278 chr8 146364022 9499601 0.06490393520342042 0.8078377398403672 chr9 141213431 7721031 0.05467632182947244 0.41130792419896406 chr10 135534747 8520368 0.06286482388165744 0.37234946314499245 chr11 135006516 8002214 0.05927279835885847 0.3577364484524627 chr12 133851895 8502115 0.06351882429456826 0.31372209216900543 chr13 115169878 7363502 0.06393600590598872 0.3100381595030583 chr14 107349540 5893770 0.054902610667917164 0.3069433631179397 chr15 102531392 4744387 0.04627253085572075 0.2631006758666493 chr16 90354753 4856914 0.05375382964081591 0.30498623101210065 chr17 81195210 3737567 0.0460318656728642 0.2911908193201798 chr18 78077248 5238064 0.0670882252407257 0.7212891416362228 chr19 59128983 2318324 0.03920791264074337 0.43614042333183894 chr20 63025520 3567674 0.05660681577875121 0.29785584351356303 chr21 48129895 2520509 0.05236888632314698 0.2998265566357765 chr22 51304566 1455785 0.028375349671606227 0.20090386156966045 chrMT 16571 28909 1.7445537384587533 1.6035201797844285 chrX 155270560 10162523 0.06545041764517369 0.3285027845038564 chrY 59373566 378537 0.006375513978729187 0.13266472729540735