| Variant ID: vg0404418363 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 4418363 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.84, T: 0.15, others allele: 0.00, population size: 99. )
GCTTTTAATGTTTGGCAAGTGAATTGTACAAATCAAGTTGGGTACTAGATATTTAATTATTATTTGTCAATATCTTTCATAACTGAATTATATCTACAAA[T/A]
TTGTCATAAATTTCTCCTCAGTCAGTAAATTTTTAAGAATACCACTGATTTGGTTGAGAGGCGATTCGATGTTTAACTGGCTATTTTGAAATGGTTCAGG
CCTGAACCATTTCAAAATAGCCAGTTAAACATCGAATCGCCTCTCAACCAAATCAGTGGTATTCTTAAAAATTTACTGACTGAGGAGAAATTTATGACAA[A/T]
TTTGTAGATATAATTCAGTTATGAAAGATATTGACAAATAATAATTAAATATCTAGTACCCAACTTGATTTGTACAATTCACTTGCCAAACATTAAAAGC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 58.10% | 41.90% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 62.80% | 37.20% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 44.10% | 55.80% | 0.07% | 0.00% | NA |
| Aus | 269 | 72.10% | 27.90% | 0.00% | 0.00% | NA |
| Indica I | 595 | 8.60% | 91.40% | 0.00% | 0.00% | NA |
| Indica II | 465 | 84.70% | 15.30% | 0.00% | 0.00% | NA |
| Indica III | 913 | 82.30% | 17.70% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 68.30% | 31.60% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 9.40% | 90.50% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 91.50% | 8.50% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 55.60% | 44.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 94.80% | 5.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 65.60% | 34.40% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0404418363 | T -> A | LOC_Os04g08280.1 | downstream_gene_variant ; 813.0bp to feature; MODIFIER | silent_mutation | Average:50.239; most accessible tissue: Zhenshan97 root, score: 63.237 | N | N | N | N |
| vg0404418363 | T -> A | LOC_Os04g08260-LOC_Os04g08280 | intergenic_region ; MODIFIER | silent_mutation | Average:50.239; most accessible tissue: Zhenshan97 root, score: 63.237 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0404418363 | NA | 1.10E-08 | mr1593 | 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 |
| vg0404418363 | NA | 5.79E-07 | mr1627 | 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 |
| vg0404418363 | NA | 4.09E-07 | mr1789 | 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 |
| vg0404418363 | NA | 3.62E-07 | mr1860_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 |
| vg0404418363 | NA | 3.76E-07 | mr1904_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 |