BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472542.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 = 16,719,678 number of mapped reads = 16,547,722 (98.97%) number of supplementary alignments = 71,942 (0.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,308,868 number of mapped paired reads (second in pair) = 8,238,854 number of mapped paired reads (both in pair) = 16,441,832 number of mapped paired reads (singletons) = 105,890 number of mapped bases = 1,630,642,774 bp number of sequenced bases = 1,630,431,892 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,367,151 duplication rate = 46.49% >>>>>>> Insert size mean insert size = 33,817.1046 std insert size = 1,808,259.0776 median insert size = 238 >>>>>>> Mapping quality mean mapping quality = 55.0707 >>>>>>> ACTG content number of A's = 445,849,728 bp (27.35%) number of C's = 372,178,834 bp (22.83%) number of T's = 443,166,493 bp (27.18%) number of G's = 368,982,855 bp (22.63%) number of N's = 253,982 bp (0.02%) GC percentage = 45.46% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 9,807,012 number of insertions = 89,703 mapped reads with insertion percentage = 0.53% number of deletions = 83,686 mapped reads with deletion percentage = 0.5% homopolymer indels = 44.65% >>>>>>> Coverage mean coverageData = 0.5267X std coverageData = 18.6815X There is a 5.13% of reference with a coverageData >= 1X There is a 2.27% of reference with a coverageData >= 2X There is a 0.99% of reference with a coverageData >= 3X There is a 0.69% of reference with a coverageData >= 4X There is a 0.5% of reference with a coverageData >= 5X There is a 0.44% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.35% of reference with a coverageData >= 9X There is a 0.34% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.3% of reference with a coverageData >= 13X There is a 0.29% of reference with a coverageData >= 14X There is a 0.29% of reference with a coverageData >= 15X There is a 0.28% of reference with a coverageData >= 16X There is a 0.27% of reference with a coverageData >= 17X There is a 0.27% of reference with a coverageData >= 18X There is a 0.26% of reference with a coverageData >= 19X There is a 0.25% of reference with a coverageData >= 20X There is a 0.25% of reference with a coverageData >= 21X There is a 0.24% of reference with a coverageData >= 22X There is a 0.24% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.23% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.21% of reference with a coverageData >= 30X There is a 0.21% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 185830942 0.7455585918078816 29.474285726402517 chr2 243199373 117795221 0.4843565982384338 18.24735546437799 chr3 198022430 186249410 0.9405470380299847 21.136791765460046 chr4 191154276 54222630 0.28365899594105864 9.882547259590059 chr5 180915260 100610117 0.5561173612441538 19.073394863114714 chr6 171115067 113736487 0.6646783886073574 20.170869846100732 chr7 159138663 51439364 0.3232361201878389 8.500034815987373 chr8 146364022 68327883 0.46683523769249796 14.589187223676888 chr9 141213431 97787122 0.6924774882071947 17.190655919421978 chr10 135534747 42134465 0.31087574170186777 9.84532058394732 chr11 135006516 72595846 0.5377210534045631 15.995674285735523 chr12 133851895 98125165 0.7330876040268238 28.46674456740334 chr13 115169878 46408699 0.40295865382439666 17.03747624723289 chr14 107349540 48349547 0.45039361137458067 23.589227558015267 chr15 102531392 38418231 0.37469725369572665 12.516904645641924 chr16 90354753 45061545 0.49871803644906204 12.685284353212936 chr17 81195210 72138790 0.8884611542971562 21.698037169610195 chr18 78077248 34571227 0.44278234550480056 31.45493821886296 chr19 59128983 33470602 0.56606084363061 14.412817376124986 chr20 63025520 32963101 0.5230119640425022 13.898093667149187 chr21 48129895 5565064 0.11562593269733915 4.314542197367322 chr22 51304566 16770957 0.3268901446315714 12.524714784911449 chrMT 16571 5484 0.33093959326534306 1.1561749551240614 chrX 155270560 66443292 0.42791944590139946 13.179248604722329 chrY 59373566 1621583 0.027311531195549212 0.7634793370815274