Variant ID: vg0430653744 (JBrowse) | Variation Type: SNP |
Chromosome: chr04 | Position: 30653744 |
Reference Allele: T | Alternative Allele: C |
Primary Allele: T | Secondary Allele: Unkown |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 395. )
CTTCGCAGTAGTCGCCGAAGAGTTCACTAGTGAATTGGGTGCCATTATCCGTAATGATACGGTTAGGCACTCCAAAACGGGCCGTGATGCCCTTAATGAA[T/C]
TTAAGTGCAGAGTGCTTATCGATCTTGACGACCGGATAAGCCTCGGGCCACTTAGTGAACTTGTCGATCGCGACATACAGATACTCAAACCCGCCCGGGG
CCCCGGGCGGGTTTGAGTATCTGTATGTCGCGATCGACAAGTTCACTAAGTGGCCCGAGGCTTATCCGGTCGTCAAGATCGATAAGCACTCTGCACTTAA[A/G]
TTCATTAAGGGCATCACGGCCCGTTTTGGAGTGCCTAACCGTATCATTACGGATAATGGCACCCAATTCACTAGTGAACTCTTCGGCGACTACTGCGAAG
Populations | Population Size | Frequency of T(primary allele) | Frequency of Unkown(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 84.40% | 0.00% | 0.21% | 15.38% | NA |
All Indica | 2759 | 99.30% | 0.00% | 0.00% | 0.69% | NA |
All Japonica | 1512 | 55.80% | 0.00% | 0.53% | 43.72% | NA |
Aus | 269 | 91.40% | 0.00% | 0.74% | 7.81% | NA |
Indica I | 595 | 99.80% | 0.00% | 0.00% | 0.17% | NA |
Indica II | 465 | 99.40% | 0.00% | 0.00% | 0.65% | NA |
Indica III | 913 | 99.90% | 0.00% | 0.00% | 0.11% | NA |
Indica Intermediate | 786 | 98.20% | 0.00% | 0.00% | 1.78% | NA |
Temperate Japonica | 767 | 64.90% | 0.00% | 0.26% | 34.81% | NA |
Tropical Japonica | 504 | 46.20% | 0.00% | 0.60% | 53.17% | NA |
Japonica Intermediate | 241 | 46.50% | 0.00% | 1.24% | 52.28% | NA |
VI/Aromatic | 96 | 81.20% | 0.00% | 0.00% | 18.75% | NA |
Intermediate | 90 | 91.10% | 0.00% | 0.00% | 8.89% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0430653744 | T -> C | LOC_Os04g51730.1 | synonymous_variant ; p.Lys206Lys; LOW | N | Average:11.428; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
vg0430653744 | T -> C | LOC_Os04g51720.1 | downstream_gene_variant ; 1346.0bp to feature; MODIFIER | N | Average:11.428; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
vg0430653744 | T -> C | LOC_Os04g51740.1 | downstream_gene_variant ; 3635.0bp to feature; MODIFIER | N | Average:11.428; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |