| Variant ID: vg0200657074 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 657074 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 127. )
GCCGCCGCCGCCGCCACGCCGCCCAACAACTCGCCGGAGCACGCCTAAGGCGTAAACAATTCTGCGACCGAGACCAGCAATACGCTGGAGTTCGACTCGA[T/G]
GATAACACGCCGGAGCACGTCCTTGTTGCAAACGGTGATGAAATTAAGAGTGAAATATTTCCTTAGGAATTGAATCCTTTGAAATTAATTCCTTTGGAAT
ATTCCAAAGGAATTAATTTCAAAGGATTCAATTCCTAAGGAAATATTTCACTCTTAATTTCATCACCGTTTGCAACAAGGACGTGCTCCGGCGTGTTATC[A/C]
TCGAGTCGAACTCCAGCGTATTGCTGGTCTCGGTCGCAGAATTGTTTACGCCTTAGGCGTGCTCCGGCGAGTTGTTGGGCGGCGTGGCGGCGGCGGCGGC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 87.80% | 9.60% | 2.64% | 0.00% | NA |
| All Indica | 2759 | 95.40% | 4.00% | 0.54% | 0.00% | NA |
| All Japonica | 1512 | 77.90% | 15.30% | 6.81% | 0.00% | NA |
| Aus | 269 | 66.90% | 31.60% | 1.49% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.17% | 0.00% | NA |
| Indica II | 465 | 81.90% | 15.90% | 2.15% | 0.00% | NA |
| Indica III | 913 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 95.80% | 3.70% | 0.51% | 0.00% | NA |
| Temperate Japonica | 767 | 90.60% | 1.40% | 7.95% | 0.00% | NA |
| Tropical Japonica | 504 | 67.70% | 28.40% | 3.97% | 0.00% | NA |
| Japonica Intermediate | 241 | 58.90% | 32.00% | 9.13% | 0.00% | NA |
| VI/Aromatic | 96 | 80.20% | 18.80% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 88.90% | 8.90% | 2.22% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0200657074 | T -> G | LOC_Os02g02170.1 | 3_prime_UTR_variant ; 53.0bp to feature; MODIFIER | silent_mutation | Average:46.266; most accessible tissue: Zhenshan97 panicle, score: 61.671 | N | N | N | N |
| vg0200657074 | T -> G | LOC_Os02g02180.1 | downstream_gene_variant ; 2616.0bp to feature; MODIFIER | silent_mutation | Average:46.266; most accessible tissue: Zhenshan97 panicle, score: 61.671 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0200657074 | 2.54E-06 | 2.54E-06 | mr1009 | 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 |
| vg0200657074 | NA | 2.18E-06 | mr1334 | 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 |
| vg0200657074 | NA | 6.37E-06 | mr1415 | 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 |
| vg0200657074 | NA | 6.37E-06 | mr1567 | 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 |
| vg0200657074 | NA | 4.06E-06 | mr1928_2 | 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 |