Variant ID: vg0203898222 (JBrowse) | Variation Type: SNP |
Chromosome: chr02 | Position: 3898222 |
Reference Allele: T | Alternative Allele: C |
Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 227. )
ACACACTTGACAGGCATCCGAATATAAAAACTCTAAAGATTACCCATCAAGTATTATGAAGATTATGGTAATAAATAAGTCGAATAGCCTAGGCCATGAC[T/C]
ATTTACCATAATGAAAATAGGTATATCACATACCAAGGAAGTGACTATAGTAAAAACAAGTCATTCCTAGTTAACCCAAACAGCTTTTGTAGCCTAAAAA
TTTTTAGGCTACAAAAGCTGTTTGGGTTAACTAGGAATGACTTGTTTTTACTATAGTCACTTCCTTGGTATGTGATATACCTATTTTCATTATGGTAAAT[A/G]
GTCATGGCCTAGGCTATTCGACTTATTTATTACCATAATCTTCATAATACTTGATGGGTAATCTTTAGAGTTTTTATATTCGGATGCCTGTCAAGTGTGT
Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 35.80% | 4.40% | 21.52% | 38.26% | NA |
All Indica | 2759 | 31.70% | 0.20% | 16.24% | 51.87% | NA |
All Japonica | 1512 | 44.20% | 12.70% | 32.61% | 10.45% | NA |
Aus | 269 | 11.50% | 0.00% | 17.10% | 71.38% | NA |
Indica I | 595 | 21.20% | 0.00% | 11.09% | 67.73% | NA |
Indica II | 465 | 17.20% | 0.40% | 18.49% | 63.87% | NA |
Indica III | 913 | 45.00% | 0.30% | 19.06% | 35.60% | NA |
Indica Intermediate | 786 | 32.70% | 0.10% | 15.52% | 51.65% | NA |
Temperate Japonica | 767 | 71.30% | 1.40% | 15.91% | 11.34% | NA |
Tropical Japonica | 504 | 6.90% | 30.20% | 54.56% | 8.33% | NA |
Japonica Intermediate | 241 | 36.10% | 12.00% | 39.83% | 12.03% | NA |
VI/Aromatic | 96 | 85.40% | 0.00% | 13.54% | 1.04% | NA |
Intermediate | 90 | 41.10% | 11.10% | 18.89% | 28.89% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0203898222 | T -> DEL | N | N | silent_mutation | Average:8.906; most accessible tissue: Callus, score: 19.376 | N | N | N | N |
vg0203898222 | T -> C | LOC_Os02g07520.1 | upstream_gene_variant ; 2780.0bp to feature; MODIFIER | silent_mutation | Average:8.906; most accessible tissue: Callus, score: 19.376 | N | N | N | N |
vg0203898222 | T -> C | LOC_Os02g07530.1 | upstream_gene_variant ; 575.0bp to feature; MODIFIER | silent_mutation | Average:8.906; most accessible tissue: Callus, score: 19.376 | N | N | N | N |
vg0203898222 | T -> C | LOC_Os02g07540.1 | downstream_gene_variant ; 3836.0bp to feature; MODIFIER | silent_mutation | Average:8.906; most accessible tissue: Callus, score: 19.376 | N | N | N | N |
vg0203898222 | T -> C | LOC_Os02g07520-LOC_Os02g07530 | intergenic_region ; MODIFIER | silent_mutation | Average:8.906; most accessible tissue: Callus, score: 19.376 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0203898222 | NA | 1.66E-06 | mr1518 | Jap_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 |