BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124852.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 132,266,496 number of mapped reads = 128,683,925 (97.29%) number of supplementary alignments = 1,726,048 (1.3%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 64,992,370 number of mapped paired reads (second in pair) = 63,691,555 number of mapped paired reads (both in pair) = 126,876,080 number of mapped paired reads (singletons) = 1,807,845 number of mapped bases = 17,513,431,581 bp number of sequenced bases = 17,498,452,955 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 48,050,785 duplication rate = 27.99% >>>>>>> Insert size mean insert size = 50,396.5023 std insert size = 2,131,597.9568 median insert size = 260 >>>>>>> Mapping quality mean mapping quality = 53.8525 >>>>>>> ACTG content number of A's = 4,996,331,629 bp (28.55%) number of C's = 3,489,086,875 bp (19.94%) number of T's = 5,089,583,282 bp (29.09%) number of G's = 3,923,411,167 bp (22.42%) number of N's = 40,002 bp (0%) GC percentage = 42.36% >>>>>>> Mismatches and indels general error rate = 0.013 number of mismatches = 217,166,372 number of insertions = 3,433,941 mapped reads with insertion percentage = 2.46% number of deletions = 7,027,248 mapped reads with deletion percentage = 5.2% homopolymer indels = 44.6% >>>>>>> Coverage mean coverageData = 5.6574X std coverageData = 53.1799X There is a 61.19% of reference with a coverageData >= 1X There is a 52.24% of reference with a coverageData >= 2X There is a 44.61% of reference with a coverageData >= 3X There is a 38.83% of reference with a coverageData >= 4X There is a 33.86% of reference with a coverageData >= 5X There is a 29.77% of reference with a coverageData >= 6X There is a 26.25% of reference with a coverageData >= 7X There is a 23.26% of reference with a coverageData >= 8X There is a 20.67% of reference with a coverageData >= 9X There is a 18.42% of reference with a coverageData >= 10X There is a 16.47% of reference with a coverageData >= 11X There is a 14.76% of reference with a coverageData >= 12X There is a 13.26% of reference with a coverageData >= 13X There is a 11.94% of reference with a coverageData >= 14X There is a 10.78% of reference with a coverageData >= 15X There is a 9.74% of reference with a coverageData >= 16X There is a 8.83% of reference with a coverageData >= 17X There is a 8.01% of reference with a coverageData >= 18X There is a 7.28% of reference with a coverageData >= 19X There is a 6.63% of reference with a coverageData >= 20X There is a 6.04% of reference with a coverageData >= 21X There is a 5.52% of reference with a coverageData >= 22X There is a 5.04% of reference with a coverageData >= 23X There is a 4.62% of reference with a coverageData >= 24X There is a 4.23% of reference with a coverageData >= 25X There is a 3.88% of reference with a coverageData >= 26X There is a 3.56% of reference with a coverageData >= 27X There is a 3.28% of reference with a coverageData >= 28X There is a 3.02% of reference with a coverageData >= 29X There is a 2.78% of reference with a coverageData >= 30X There is a 2.56% of reference with a coverageData >= 31X There is a 2.37% of reference with a coverageData >= 32X There is a 2.19% of reference with a coverageData >= 33X There is a 2.02% of reference with a coverageData >= 34X There is a 1.87% of reference with a coverageData >= 35X There is a 1.74% of reference with a coverageData >= 36X There is a 1.61% of reference with a coverageData >= 37X There is a 1.5% of reference with a coverageData >= 38X There is a 1.39% of reference with a coverageData >= 39X There is a 1.29% of reference with a coverageData >= 40X There is a 1.2% of reference with a coverageData >= 41X There is a 1.12% of reference with a coverageData >= 42X There is a 1.05% of reference with a coverageData >= 43X There is a 0.98% of reference with a coverageData >= 44X There is a 0.91% of reference with a coverageData >= 45X There is a 0.85% of reference with a coverageData >= 46X There is a 0.8% of reference with a coverageData >= 47X There is a 0.74% of reference with a coverageData >= 48X There is a 0.7% of reference with a coverageData >= 49X There is a 0.65% of reference with a coverageData >= 50X There is a 0.61% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1609468209 6.45722848168952 39.60188423771527 chr2 243199373 1448128058 5.954489274115028 66.10198632898098 chr3 198022430 1175566504 5.936532058514786 9.792968366960952 chr4 191154276 829774263 4.3408616347143605 90.10931755037963 chr5 180915260 932779131 5.15588972981052 10.01690049814861 chr6 171115067 1004318502 5.86925815246883 22.533735241066456 chr7 159138663 1242734082 7.809127326902326 43.6667581396933 chr8 146364022 1162065171 7.939554783483608 19.71137253080199 chr9 141213431 676855525 4.793138444458587 69.26374510298513 chr10 135534747 843161545 6.220999143489013 133.84449900067906 chr11 135006516 608882918 4.510026153108047 15.794353090965142 chr12 133851895 843579912 6.302338207464302 10.21170371512141 chr13 115169878 364209105 3.1623642511803305 6.181368974375646 chr14 107349540 726005362 6.7630039402125055 12.61722403355731 chr15 102531392 481908318 4.7001050956179355 8.604206110246787 chr16 90354753 651976008 7.21573560164566 72.86815208086567 chr17 81195210 424961064 5.233819384173032 49.55168057418812 chr18 78077248 247633102 3.1716422945644807 53.598926425843885 chr19 59128983 346012747 5.851829837830967 21.942221336834518 chr20 63025520 443596366 7.038361063899195 28.739388260604375 chr21 48129895 175997386 3.6567165999427176 40.23064227133079 chr22 51304566 175560625 3.4219298336916055 9.099622448799433 chrMT 16571 824670 49.76585601351759 25.99519989074987 chrX 155270560 803315205 5.173647889207071 13.25354186535 chrY 59373566 294117803 4.953682637152029 128.7720450451119