| Variant ID: vg0123927216 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 23927216 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 119. )
TTAAAGTGGTGCTAAACTTTAGTCCCTCTCACAAAAATATAAGTTCTTACCATAGGGACTTATACTTTTGTGAGAGGGACTAAATTTAGTCCCTAGTTCC[C/T]
AAACACCCCCTTAAAATGGTTACAGACAAAAAAAAATAAAATAAAAAAAGAAACATAGAAATGGAAACGAAAACGATTTGCTTTGCCGCGTATCGATCAT
ATGATCGATACGCGGCAAAGCAAATCGTTTTCGTTTCCATTTCTATGTTTCTTTTTTTATTTTATTTTTTTTTGTCTGTAACCATTTTAAGGGGGTGTTT[G/A]
GGAACTAGGGACTAAATTTAGTCCCTCTCACAAAAGTATAAGTCCCTATGGTAAGAACTTATATTTTTGTGAGAGGGACTAAAGTTTAGCACCACTTTAA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 77.40% | 22.20% | 0.38% | 0.00% | NA |
| All Indica | 2759 | 71.40% | 28.50% | 0.11% | 0.00% | NA |
| All Japonica | 1512 | 84.50% | 14.80% | 0.66% | 0.00% | NA |
| Aus | 269 | 92.60% | 6.30% | 1.12% | 0.00% | NA |
| Indica I | 595 | 40.70% | 59.30% | 0.00% | 0.00% | NA |
| Indica II | 465 | 89.00% | 11.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 75.10% | 24.80% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 79.80% | 20.00% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 99.10% | 0.80% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 58.50% | 39.90% | 1.59% | 0.00% | NA |
| Japonica Intermediate | 241 | 92.50% | 7.10% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 89.60% | 9.40% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 84.40% | 14.40% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0123927216 | C -> T | LOC_Os01g42234.2 | upstream_gene_variant ; 2475.0bp to feature; MODIFIER | silent_mutation | Average:64.152; most accessible tissue: Zhenshan97 panicle, score: 82.888 | N | N | N | N |
| vg0123927216 | C -> T | LOC_Os01g42220.1 | downstream_gene_variant ; 4354.0bp to feature; MODIFIER | silent_mutation | Average:64.152; most accessible tissue: Zhenshan97 panicle, score: 82.888 | N | N | N | N |
| vg0123927216 | C -> T | LOC_Os01g42234.1 | intron_variant ; MODIFIER | silent_mutation | Average:64.152; most accessible tissue: Zhenshan97 panicle, score: 82.888 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0123927216 | NA | 1.56E-06 | mr1830 | Jap_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 |
| vg0123927216 | NA | 1.62E-07 | mr1925 | 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 |
| vg0123927216 | 8.39E-08 | 1.23E-09 | mr1925 | 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 |
| vg0123927216 | NA | 8.11E-07 | mr1498_2 | Jap_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 |