BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714141.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 884,440 number of mapped reads = 399,401 (45.16%) number of supplementary alignments = 13,921 (1.57%) number of secondary alignments = 0 number of mapped bases = 50,498,393 bp number of sequenced bases = 49,502,310 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 324,749 duplication rate = 42.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 52.3894 >>>>>>> ACTG content number of A's = 13,255,028 bp (26.78%) number of C's = 10,460,299 bp (21.13%) number of T's = 12,554,734 bp (25.36%) number of G's = 13,231,884 bp (26.73%) number of N's = 365 bp (0%) GC percentage = 47.86% >>>>>>> Mismatches and indels general error rate = 0.0424 number of mismatches = 1,922,576 number of insertions = 53,392 mapped reads with insertion percentage = 12.64% number of deletions = 166,575 mapped reads with deletion percentage = 39.9% homopolymer indels = 29.38% >>>>>>> Coverage mean coverageData = 0.0163X std coverageData = 3.2455X There is a 0.06% of reference with a coverageData >= 1X There is a 0.05% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% 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 4487780 0.018005090546996068 2.023656119159876 chr2 243199373 6799922 0.02796027767719615 9.873914800405696 chr3 198022430 2437859 0.012311024564237496 1.2044716037823788 chr4 191154276 2377251 0.01243629517343363 1.375579679260426 chr5 180915260 2558036 0.014139415326269326 1.3137704882446635 chr6 171115067 1968097 0.011501599680874391 1.1354182966270538 chr7 159138663 1896521 0.0119174119239647 1.2582711370861555 chr8 146364022 2565954 0.017531316541711323 2.306698709004337 chr9 141213431 1967728 0.01393442526015815 1.5404997935086073 chr10 135534747 2762180 0.020379866131302847 1.9777799341806224 chr11 135006516 2428266 0.01798628741741621 2.3207905606765693 chr12 133851895 1960094 0.014643752335370373 1.641023886578794 chr13 115169878 1430839 0.012423725932921454 1.5424237246696355 chr14 107349540 1640377 0.015280708235917918 1.6002268807263502 chr15 102531392 1427614 0.013923677150506257 1.5810034496147891 chr16 90354753 1466834 0.016234165346011183 1.7034752830425697 chr17 81195210 1856259 0.022861681126263484 2.4463920027199255 chr18 78077248 1109817 0.014214345772023112 1.3403514764664757 chr19 59128983 892564 0.015095202973472418 1.6318392946265738 chr20 63025520 1160653 0.018415603711004685 1.4843217180563641 chr21 48129895 371491 0.0077185084239223874 0.9105837569847952 chr22 51304566 512099 0.009981548231009302 1.0862365840556258 chrMT 16571 491947 29.687224669603523 273.78770900319233 chrX 155270560 3720909 0.023964034134996356 1.505104546203908 chrY 59373566 207302 0.00349148643017332 0.46804556411706066