| Variant ID: vg0320989254 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 20989254 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 313. )
TACTTTTTGCTAGCCATGCACATAGTACTCATAGTCACCAGGCTAAGTATTGTTCAATCCTAGTGAGGTACATAAGTAATTAGTATGGTTTTTTAGCAAG[A/G]
CAGGGACTAAGATAAAACAGAGTTAAAACAATCACCAATATAGAGGAATATGATGAAACAATGGAGGAGAGCATTTTTTTAATCATTATTCCCTTTTTTT
AAAAAAAGGGAATAATGATTAAAAAAATGCTCTCCTCCATTGTTTCATCATATTCCTCTATATTGGTGATTGTTTTAACTCTGTTTTATCTTAGTCCCTG[T/C]
CTTGCTAAAAAACCATACTAATTACTTATGTACCTCACTAGGATTGAACAATACTTAGCCTGGTGACTATGAGTACTATGTGCATGGCTAGCAAAAAGTA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 92.10% | 7.40% | 0.42% | 0.00% | NA |
| All Indica | 2759 | 99.10% | 0.80% | 0.11% | 0.00% | NA |
| All Japonica | 1512 | 85.60% | 13.40% | 0.99% | 0.00% | NA |
| Aus | 269 | 89.20% | 10.40% | 0.37% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 97.60% | 2.00% | 0.38% | 0.00% | NA |
| Temperate Japonica | 767 | 97.90% | 1.40% | 0.65% | 0.00% | NA |
| Tropical Japonica | 504 | 74.60% | 24.40% | 0.99% | 0.00% | NA |
| Japonica Intermediate | 241 | 69.30% | 28.60% | 2.07% | 0.00% | NA |
| VI/Aromatic | 96 | 9.40% | 89.60% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 87.80% | 12.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0320989254 | A -> G | LOC_Os03g37830.1 | upstream_gene_variant ; 3495.0bp to feature; MODIFIER | silent_mutation | Average:56.804; most accessible tissue: Zhenshan97 young leaf, score: 80.325 | N | N | N | N |
| vg0320989254 | A -> G | LOC_Os03g37830-LOC_Os03g37840 | intergenic_region ; MODIFIER | silent_mutation | Average:56.804; most accessible tissue: Zhenshan97 young leaf, score: 80.325 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0320989254 | NA | 8.64E-06 | mr1135 | 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 |
| vg0320989254 | 1.06E-07 | 1.95E-10 | mr1217 | 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 |
| vg0320989254 | 3.27E-07 | 1.95E-09 | mr1845 | 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 |