BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038399.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 = 18,698,730 number of mapped reads = 17,874,388 (95.59%) number of supplementary alignments = 309,401 (1.65%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,035,503 number of mapped paired reads (second in pair) = 8,838,885 number of mapped paired reads (both in pair) = 17,622,956 number of mapped paired reads (singletons) = 251,432 number of mapped bases = 2,415,847,006 bp number of sequenced bases = 2,414,154,155 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,712,761 duplication rate = 14.52% >>>>>>> Insert size mean insert size = 94,746.1915 std insert size = 2,934,937.3577 median insert size = 243 >>>>>>> Mapping quality mean mapping quality = 53.5283 >>>>>>> ACTG content number of A's = 690,486,529 bp (28.6%) number of C's = 480,336,481 bp (19.9%) number of T's = 703,025,473 bp (29.12%) number of G's = 540,104,870 bp (22.37%) number of N's = 200,802 bp (0.01%) GC percentage = 42.27% >>>>>>> Mismatches and indels general error rate = 0.013 number of mismatches = 30,184,908 number of insertions = 427,868 mapped reads with insertion percentage = 2.27% number of deletions = 829,405 mapped reads with deletion percentage = 4.46% homopolymer indels = 46.83% >>>>>>> Coverage mean coverageData = 0.7804X std coverageData = 11.7919X There is a 29.95% of reference with a coverageData >= 1X There is a 17.32% of reference with a coverageData >= 2X There is a 9.68% of reference with a coverageData >= 3X There is a 5.92% of reference with a coverageData >= 4X There is a 3.55% of reference with a coverageData >= 5X There is a 2.22% of reference with a coverageData >= 6X There is a 1.4% of reference with a coverageData >= 7X There is a 0.9% of reference with a coverageData >= 8X There is a 0.59% of reference with a coverageData >= 9X There is a 0.39% of reference with a coverageData >= 10X There is a 0.27% of reference with a coverageData >= 11X There is a 0.19% of reference with a coverageData >= 12X There is a 0.13% of reference with a coverageData >= 13X There is a 0.1% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% 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 0.03% 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 0.02% of reference with a coverageData >= 35X There is a 0.02% 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 185935174 0.745976773313636 17.026831586275815 chr2 243199373 212399610 0.8733559111601822 11.0653920411871 chr3 198022430 159718199 0.8065662006066686 1.8191739125771753 chr4 191154276 160440518 0.8393247661381114 9.256061540636841 chr5 180915260 144652078 0.7995570854553673 1.6718243964567965 chr6 171115067 140590339 0.8216128565697841 7.842651396736597 chr7 159138663 128180418 0.80546371060061 10.810946310976728 chr8 146364022 121387843 0.8293557483682704 3.6147012202835107 chr9 141213431 100405701 0.7110209014042014 16.04164535032986 chr10 135534747 139649342 1.0303582298345972 34.691979448592384 chr11 135006516 111194434 0.8236227205507621 7.289537570788961 chr12 133851895 102656951 0.7669443230519822 1.7567775766238216 chr13 115169878 73261582 0.6361175619201402 1.4587110397088972 chr14 107349540 68375941 0.6369467535678308 1.6540347760183198 chr15 102531392 65955067 0.6432670591266332 1.4912449614368115 chr16 90354753 87147286 0.9645014025991527 18.33401731815989 chr17 81195210 58679206 0.7226929519610824 12.14420127444861 chr18 78077248 68094799 0.8721465054710945 12.9440652456405 chr19 59128983 32604372 0.551411006003604 8.241814585859535 chr20 63025520 49150624 0.7798527326708292 3.060474180610205 chr21 48129895 30552408 0.6347906638898755 4.500271709668642 chr22 51304566 22608171 0.44066586588024154 1.30049799316652 chrMT 16571 2924154 176.46213264136142 97.96892069474046 chrX 155270560 140231494 0.9031428366072745 3.878790722370975 chrY 59373566 9051295 0.15244654498266114 11.506617297242807