BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038389.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 16,691,028 number of mapped reads = 16,078,857 (96.33%) number of supplementary alignments = 277,961 (1.67%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,149,198 number of mapped paired reads (second in pair) = 7,929,659 number of mapped paired reads (both in pair) = 15,797,748 number of mapped paired reads (singletons) = 281,109 number of mapped bases = 2,160,684,796 bp number of sequenced bases = 2,159,042,414 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,268,027 duplication rate = 13.85% >>>>>>> Insert size mean insert size = 82,918.245 std insert size = 2,738,052.1191 median insert size = 248 >>>>>>> Mapping quality mean mapping quality = 53.4321 >>>>>>> ACTG content number of A's = 621,379,676 bp (28.78%) number of C's = 423,969,446 bp (19.64%) number of T's = 634,656,948 bp (29.4%) number of G's = 478,865,979 bp (22.18%) number of N's = 170,365 bp (0.01%) GC percentage = 41.82% >>>>>>> Mismatches and indels general error rate = 0.014 number of mismatches = 29,178,534 number of insertions = 409,820 mapped reads with insertion percentage = 2.4% number of deletions = 808,688 mapped reads with deletion percentage = 4.83% homopolymer indels = 46.64% >>>>>>> Coverage mean coverageData = 0.698X std coverageData = 10.2465X There is a 27.91% of reference with a coverageData >= 1X There is a 15.62% of reference with a coverageData >= 2X There is a 8.5% of reference with a coverageData >= 3X There is a 5.05% of reference with a coverageData >= 4X There is a 2.97% of reference with a coverageData >= 5X There is a 1.82% of reference with a coverageData >= 6X There is a 1.12% of reference with a coverageData >= 7X There is a 0.71% of reference with a coverageData >= 8X There is a 0.46% of reference with a coverageData >= 9X There is a 0.31% of reference with a coverageData >= 10X There is a 0.21% of reference with a coverageData >= 11X There is a 0.15% of reference with a coverageData >= 12X There is a 0.11% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 169247816 0.6790266572695921 15.842693288782739 chr2 243199373 191676538 0.7881456914775845 10.105381266780814 chr3 198022430 143096146 0.7226259469697448 1.652960090556988 chr4 191154276 145331225 0.7602823648056923 9.765437598564693 chr5 180915260 129358126 0.7150205350283885 1.564380272026261 chr6 171115067 124674975 0.7286031393132669 6.728198630123408 chr7 159138663 113529502 0.7133998731659572 9.630432872966868 chr8 146364022 108698350 0.7426575774202214 3.277368151775459 chr9 141213431 89980326 0.6371938232985784 15.31032058066975 chr10 135534747 122781777 0.9059062691871923 27.331069351339327 chr11 135006516 99380888 0.7361191959060702 6.491423074495988 chr12 133851895 92466165 0.6908095324313488 1.6331991777747752 chr13 115169878 65481768 0.5685667913966185 1.3543710746513191 chr14 107349540 61638121 0.5741815102328338 1.533750277329647 chr15 102531392 58007831 0.5657567879308613 1.3700212101096974 chr16 90354753 73319415 0.8114616283661359 13.881332332466622 chr17 81195210 53637277 0.6605965672112923 11.18023440270304 chr18 78077248 60209676 0.7711552026014031 11.760814469866498 chr19 59128983 29930580 0.5061913545849419 7.171207100053547 chr20 63025520 42987676 0.6820677719120762 3.1038652587459246 chr21 48129895 27791120 0.577419086411886 4.6941864231558785 chr22 51304566 20075695 0.3913042554535984 1.2437972359087708 chrMT 16571 3360993 202.8237885462555 103.61273945660339 chrX 155270560 125287049 0.8068950675517625 3.3925100997652327 chrY 59373566 8735761 0.14713215978976232 11.207184872323724