BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124821.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 = 29,626,840 number of mapped reads = 29,406,686 (99.26%) number of supplementary alignments = 141,621 (0.48%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,711,177 number of mapped paired reads (second in pair) = 14,695,509 number of mapped paired reads (both in pair) = 29,327,488 number of mapped paired reads (singletons) = 79,198 number of mapped bases = 2,699,320,363 bp number of sequenced bases = 2,697,788,560 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,709,223 duplication rate = 5.3% >>>>>>> Insert size mean insert size = 82,093.6225 std insert size = 2,763,207.6972 median insert size = 172 >>>>>>> Mapping quality mean mapping quality = 52.7381 >>>>>>> ACTG content number of A's = 769,084,879 bp (28.51%) number of C's = 538,879,112 bp (19.97%) number of T's = 791,564,084 bp (29.34%) number of G's = 598,240,812 bp (22.18%) number of N's = 19,673 bp (0%) GC percentage = 42.15% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 18,720,224 number of insertions = 436,541 mapped reads with insertion percentage = 1.45% number of deletions = 896,903 mapped reads with deletion percentage = 2.99% homopolymer indels = 46.63% >>>>>>> Coverage mean coverageData = 0.872X std coverageData = 7.3288X There is a 31.71% of reference with a coverageData >= 1X There is a 18.58% of reference with a coverageData >= 2X There is a 11.02% of reference with a coverageData >= 3X There is a 6.88% of reference with a coverageData >= 4X There is a 4.41% of reference with a coverageData >= 5X There is a 2.9% of reference with a coverageData >= 6X There is a 1.95% of reference with a coverageData >= 7X There is a 1.34% of reference with a coverageData >= 8X There is a 0.94% of reference with a coverageData >= 9X There is a 0.68% of reference with a coverageData >= 10X There is a 0.5% of reference with a coverageData >= 11X There is a 0.37% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.23% of reference with a coverageData >= 14X There is a 0.18% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.13% of reference with a coverageData >= 17X There is a 0.11% of reference with a coverageData >= 18X There is a 0.1% of reference with a coverageData >= 19X There is a 0.09% of reference with a coverageData >= 20X There is a 0.08% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.06% of reference with a coverageData >= 25X There is a 0.06% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.05% of reference with a coverageData >= 28X There is a 0.05% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.04% of reference with a coverageData >= 31X There is a 0.04% of reference with a coverageData >= 32X There is a 0.04% of reference with a coverageData >= 33X There is a 0.04% of reference with a coverageData >= 34X There is a 0.04% of reference with a coverageData >= 35X There is a 0.04% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.03% of reference with a coverageData >= 39X There is a 0.03% of reference with a coverageData >= 40X There is a 0.03% of reference with a coverageData >= 41X There is a 0.03% of reference with a coverageData >= 42X There is a 0.03% of reference with a coverageData >= 43X There is a 0.03% of reference with a coverageData >= 44X There is a 0.03% of reference with a coverageData >= 45X There is a 0.03% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 205752442 0.8254841700073438 9.06657385960626 chr2 243199373 234951491 0.9660859240784309 8.049006884075654 chr3 198022430 178948147 0.9036761492119857 2.0393512046201905 chr4 191154276 119338940 0.6243069341540651 3.503861490418373 chr5 180915260 229992069 1.2712695932891453 2.3810695924299914 chr6 171115067 171981421 1.0050629907417796 5.925108549681346 chr7 159138663 217951082 1.3695671302705366 11.14493057626357 chr8 146364022 153129943 1.046226667643774 6.249339096138813 chr9 141213431 114138620 0.8082702841488215 8.550139448704687 chr10 135534747 152494860 1.125134796614185 18.246641867103932 chr11 135006516 121303126 0.898498306555811 4.037444841460357 chr12 133851895 118532595 0.8855503689357554 1.8960199144006897 chr13 115169878 46479520 0.4035735802377076 1.121406936623464 chr14 107349540 58257584 0.5426905788324756 1.8536853185168578 chr15 102531392 66184516 0.6455049005869344 1.5363674450882026 chr16 90354753 115790566 1.2815105144496384 14.182862339211926 chr17 81195210 61833749 0.7615442955317192 8.773961947988147 chr18 78077248 77419267 0.991572692213742 8.814938968660213 chr19 59128983 45171744 0.7639526626054096 5.041803594256688 chr20 63025520 75273274 1.19433007454758 2.442174380586363 chr21 48129895 25115691 0.5218314106024956 1.9782465995469052 chr22 51304566 22637906 0.4412454439240359 1.5251639855453087 chrMT 16571 286131 17.26697242170056 10.149296083873296 chrX 155270560 81186453 0.5228708713358153 2.34541530017376 chrY 59373566 5169226 0.08706275112395978 5.320122360200041