Variant ID: vg1213201263 (JBrowse) | Variation Type: SNP |
Chromosome: chr12 | Position: 13201263 |
Reference Allele: A | Alternative Allele: G |
Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.81, A: 0.21, others allele: 0.00, population size: 136. )
CAAGAATCAACTCCACAAAGCTCAGCAAACAATCCTTTCAGCCAAACTGATTCTTTACATGTTTCAGCAATAGCCATGTATTCTGATTCAGTGGTAGACT[A/G]
GGCAACAACAGGCTGCAATGTTGCCTTCCAACTCACAGCACAACTACCAATGGTAAACACATAACCTGTGAGTGACCTTCTCTTATCCAAATCTGCAGCA
TGCTGCAGATTTGGATAAGAGAAGGTCACTCACAGGTTATGTGTTTACCATTGGTAGTTGTGCTGTGAGTTGGAAGGCAACATTGCAGCCTGTTGTTGCC[T/C]
AGTCTACCACTGAATCAGAATACATGGCTATTGCTGAAACATGTAAAGAATCAGTTTGGCTGAAAGGATTGTTTGCTGAGCTTTGTGGAGTTGATTCTTG
Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 37.10% | 0.50% | 33.14% | 29.28% | NA |
All Indica | 2759 | 17.90% | 0.80% | 49.29% | 32.00% | NA |
All Japonica | 1512 | 60.70% | 0.00% | 7.87% | 31.42% | NA |
Aus | 269 | 92.20% | 0.00% | 4.83% | 2.97% | NA |
Indica I | 595 | 10.60% | 0.50% | 44.37% | 44.54% | NA |
Indica II | 465 | 18.70% | 0.20% | 45.59% | 35.48% | NA |
Indica III | 913 | 17.30% | 1.10% | 57.39% | 24.21% | NA |
Indica Intermediate | 786 | 23.70% | 1.00% | 45.80% | 29.52% | NA |
Temperate Japonica | 767 | 81.70% | 0.00% | 2.35% | 15.91% | NA |
Tropical Japonica | 504 | 32.90% | 0.00% | 15.48% | 51.59% | NA |
Japonica Intermediate | 241 | 51.90% | 0.00% | 9.54% | 38.59% | NA |
VI/Aromatic | 96 | 46.90% | 2.10% | 47.92% | 3.12% | NA |
Intermediate | 90 | 52.20% | 0.00% | 31.11% | 16.67% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg1213201263 | A -> DEL | N | N | silent_mutation | Average:14.359; most accessible tissue: Callus, score: 26.559 | N | N | N | N |
vg1213201263 | A -> G | LOC_Os12g23300.1 | upstream_gene_variant ; 4078.0bp to feature; MODIFIER | silent_mutation | Average:14.359; most accessible tissue: Callus, score: 26.559 | N | N | N | N |
vg1213201263 | A -> G | LOC_Os12g23310.1 | downstream_gene_variant ; 1076.0bp to feature; MODIFIER | silent_mutation | Average:14.359; most accessible tissue: Callus, score: 26.559 | N | N | N | N |
vg1213201263 | A -> G | LOC_Os12g23320.1 | intron_variant ; MODIFIER | silent_mutation | Average:14.359; most accessible tissue: Callus, score: 26.559 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1213201263 | NA | 2.79E-08 | mr1030 | All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
vg1213201263 | NA | 7.15E-06 | mr1037 | Ind_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
vg1213201263 | NA | 6.94E-06 | mr1155 | Ind_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |