| Variant ID: vg0808350901 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 8350901 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TATACAAAAGGTAAAGCCGTTGCCCATGCTGGCTTGTGGTTGGCACGGTTAATGTTTCATAACCGAAACTCGTGAACCGGTCCTTAATTGTCATGAGCAC[G/A]
ACCATCAAAACCATGTGCTCACAACCCACCATTATCAAGTTTTAGTTGGCAAGTAATTAATTAACCACTCACGATTGACCATCGTGAGCTTCCATTAAAT
ATTTAATGGAAGCTCACGATGGTCAATCGTGAGTGGTTAATTAATTACTTGCCAACTAAAACTTGATAATGGTGGGTTGTGAGCACATGGTTTTGATGGT[C/T]
GTGCTCATGACAATTAAGGACCGGTTCACGAGTTTCGGTTATGAAACATTAACCGTGCCAACCACAAGCCAGCATGGGCAACGGCTTTACCTTTTGTATA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 39.70% | 3.00% | 5.42% | 51.88% | NA |
| All Indica | 2759 | 17.10% | 3.80% | 7.21% | 71.87% | NA |
| All Japonica | 1512 | 88.10% | 0.10% | 0.07% | 11.71% | NA |
| Aus | 269 | 6.30% | 8.90% | 15.99% | 68.77% | NA |
| Indica I | 595 | 15.60% | 1.70% | 4.03% | 78.66% | NA |
| Indica II | 465 | 34.40% | 1.50% | 5.38% | 58.71% | NA |
| Indica III | 913 | 4.60% | 6.80% | 11.17% | 77.44% | NA |
| Indica Intermediate | 786 | 22.40% | 3.40% | 6.11% | 68.07% | NA |
| Temperate Japonica | 767 | 98.70% | 0.00% | 0.00% | 1.30% | NA |
| Tropical Japonica | 504 | 76.80% | 0.20% | 0.00% | 23.02% | NA |
| Japonica Intermediate | 241 | 78.00% | 0.40% | 0.41% | 21.16% | NA |
| VI/Aromatic | 96 | 10.40% | 6.20% | 10.42% | 72.92% | NA |
| Intermediate | 90 | 52.20% | 3.30% | 3.33% | 41.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0808350901 | G -> A | LOC_Os08g13930.1 | upstream_gene_variant ; 4234.0bp to feature; MODIFIER | silent_mutation | Average:5.652; most accessible tissue: Minghui63 young leaf, score: 9.976 | N | N | N | N |
| vg0808350901 | G -> A | LOC_Os08g13940.1 | upstream_gene_variant ; 1945.0bp to feature; MODIFIER | silent_mutation | Average:5.652; most accessible tissue: Minghui63 young leaf, score: 9.976 | N | N | N | N |
| vg0808350901 | G -> A | LOC_Os08g13950.1 | upstream_gene_variant ; 4502.0bp to feature; MODIFIER | silent_mutation | Average:5.652; most accessible tissue: Minghui63 young leaf, score: 9.976 | N | N | N | N |
| vg0808350901 | G -> A | LOC_Os08g13940-LOC_Os08g13950 | intergenic_region ; MODIFIER | silent_mutation | Average:5.652; most accessible tissue: Minghui63 young leaf, score: 9.976 | N | N | N | N |
| vg0808350901 | G -> DEL | N | N | silent_mutation | Average:5.652; most accessible tissue: Minghui63 young leaf, score: 9.976 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0808350901 | NA | 7.91E-06 | mr1274 | 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 |
| vg0808350901 | 6.30E-07 | NA | mr1173_2 | 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 |
| vg0808350901 | 3.41E-06 | 3.41E-06 | mr1173_2 | Ind_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 |