BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472448.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 = 17,734,958 number of mapped reads = 17,567,064 (99.05%) number of supplementary alignments = 71,175 (0.4%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,811,654 number of mapped paired reads (second in pair) = 8,755,410 number of mapped paired reads (both in pair) = 17,467,584 number of mapped paired reads (singletons) = 99,480 number of mapped bases = 1,725,568,532 bp number of sequenced bases = 1,725,364,785 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,048,226 duplication rate = 47.12% >>>>>>> Insert size mean insert size = 18,392.6048 std insert size = 1,313,691.4235 median insert size = 226 >>>>>>> Mapping quality mean mapping quality = 54.7686 >>>>>>> ACTG content number of A's = 473,568,714 bp (27.45%) number of C's = 390,036,722 bp (22.61%) number of T's = 475,005,324 bp (27.53%) number of G's = 386,543,532 bp (22.4%) number of N's = 210,493 bp (0.01%) GC percentage = 45.01% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 9,591,093 number of insertions = 111,624 mapped reads with insertion percentage = 0.63% number of deletions = 87,658 mapped reads with deletion percentage = 0.49% homopolymer indels = 46.16% >>>>>>> Coverage mean coverageData = 0.5574X std coverageData = 17.4016X There is a 4.73% of reference with a coverageData >= 1X There is a 2.01% of reference with a coverageData >= 2X There is a 0.88% of reference with a coverageData >= 3X There is a 0.66% of reference with a coverageData >= 4X There is a 0.51% of reference with a coverageData >= 5X There is a 0.46% of reference with a coverageData >= 6X There is a 0.43% of reference with a coverageData >= 7X There is a 0.4% of reference with a coverageData >= 8X There is a 0.39% of reference with a coverageData >= 9X There is a 0.37% of reference with a coverageData >= 10X There is a 0.36% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.34% of reference with a coverageData >= 13X There is a 0.33% of reference with a coverageData >= 14X There is a 0.32% of reference with a coverageData >= 15X There is a 0.31% of reference with a coverageData >= 16X There is a 0.3% of reference with a coverageData >= 17X There is a 0.3% of reference with a coverageData >= 18X There is a 0.29% of reference with a coverageData >= 19X There is a 0.28% of reference with a coverageData >= 20X There is a 0.28% of reference with a coverageData >= 21X There is a 0.27% of reference with a coverageData >= 22X There is a 0.27% of reference with a coverageData >= 23X There is a 0.26% of reference with a coverageData >= 24X There is a 0.26% of reference with a coverageData >= 25X There is a 0.25% of reference with a coverageData >= 26X There is a 0.25% of reference with a coverageData >= 27X There is a 0.24% of reference with a coverageData >= 28X There is a 0.24% of reference with a coverageData >= 29X There is a 0.24% of reference with a coverageData >= 30X There is a 0.23% of reference with a coverageData >= 31X There is a 0.23% of reference with a coverageData >= 32X There is a 0.22% of reference with a coverageData >= 33X There is a 0.22% of reference with a coverageData >= 34X There is a 0.22% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.21% of reference with a coverageData >= 38X There is a 0.21% of reference with a coverageData >= 39X There is a 0.2% of reference with a coverageData >= 40X There is a 0.2% of reference with a coverageData >= 41X There is a 0.2% of reference with a coverageData >= 42X There is a 0.2% of reference with a coverageData >= 43X There is a 0.19% of reference with a coverageData >= 44X There is a 0.19% of reference with a coverageData >= 45X There is a 0.19% of reference with a coverageData >= 46X There is a 0.19% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.18% of reference with a coverageData >= 49X There is a 0.18% of reference with a coverageData >= 50X There is a 0.18% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 167457106 0.6718422819897407 20.83832525960362 chr2 243199373 161901205 0.6657139079055109 21.01801522119496 chr3 198022430 112449172 0.5678607822356285 12.448724180319374 chr4 191154276 65226579 0.34122479687558754 14.744627771830347 chr5 180915260 58476107 0.3232237402195923 11.635160516547057 chr6 171115067 124284106 0.7263188927717277 15.316652198487986 chr7 159138663 106446277 0.6688901049771921 20.213131176682342 chr8 146364022 141802419 0.9688338504390102 28.461585475375575 chr9 141213431 57386198 0.4063791779126165 10.779755955969707 chr10 135534747 32882396 0.24261229483831184 8.612835046067994 chr11 135006516 46283832 0.34282665290022 10.823986253341612 chr12 133851895 77617752 0.5798778717327835 14.42560073046293 chr13 115169878 67896362 0.5895322907262261 20.72759382196646 chr14 107349540 33225499 0.30950760478340195 11.0260784362504 chr15 102531392 25402324 0.2477516739458682 7.932772517447813 chr16 90354753 92955307 1.0287815960273834 24.63818377538033 chr17 81195210 85697869 1.0554547368003606 24.160999844366685 chr18 78077248 5442309 0.06970416016712064 1.8925384106471195 chr19 59128983 40770374 0.6895159011951888 15.336871179769432 chr20 63025520 77531263 1.2301566571763312 29.808727422123308 chr21 48129895 22137287 0.45994879066326655 21.77889275710265 chr22 51304566 17700805 0.3450142234903615 12.169464532700552 chrMT 16571 1652 0.09969223341982983 0.5329812963328902 chrX 155270560 104276469 0.6715791390203011 19.509294556731255 chrY 59373566 317863 0.005353611403431622 0.36116231352732114