| Variant ID: vg0301154581 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 1154581 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.91, G: 0.10, others allele: 0.00, population size: 245. )
CGCTTGGAGCATCTAGCGCCTTCGTATTTCGTATATAGCTCATCATCTCTCTTAAATTAGTCAGTGCAGTGTGAGGGGGAACAGTTTAAGAAAAAAGAAC[G/A]
AAGCAGCAACGTACCCAAAAAAAATATTCTTTCTAGGTTGATGGTTTTTTCTTGCTTCGATTTGCTTTGCCTTTTTCTCTTGTGCTTAATTATAATTAAG
CTTAATTATAATTAAGCACAAGAGAAAAAGGCAAAGCAAATCGAAGCAAGAAAAAACCATCAACCTAGAAAGAATATTTTTTTTGGGTACGTTGCTGCTT[C/T]
GTTCTTTTTTCTTAAACTGTTCCCCCTCACACTGCACTGACTAATTTAAGAGAGATGATGAGCTATATACGAAATACGAAGGCGCTAGATGCTCCAAGCG
| 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 | 60.30% | 39.40% | 0.06% | 0.21% | NA |
| All Indica | 2759 | 97.00% | 2.90% | 0.07% | 0.11% | NA |
| All Japonica | 1512 | 0.90% | 98.90% | 0.00% | 0.20% | NA |
| Aus | 269 | 24.50% | 74.70% | 0.00% | 0.74% | NA |
| Indica I | 595 | 98.20% | 1.80% | 0.00% | 0.00% | NA |
| Indica II | 465 | 94.00% | 5.80% | 0.00% | 0.22% | NA |
| Indica III | 913 | 99.20% | 0.70% | 0.00% | 0.11% | NA |
| Indica Intermediate | 786 | 95.20% | 4.50% | 0.25% | 0.13% | NA |
| Temperate Japonica | 767 | 0.40% | 99.60% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 1.00% | 98.80% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 2.10% | 97.10% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 52.10% | 46.90% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 51.10% | 46.70% | 1.11% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0301154581 | G -> A | LOC_Os03g02900.1 | 3_prime_UTR_variant ; 265.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0301154581 | G -> DEL | N | N | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0301154581 | NA | 1.57E-06 | mr1020_2 | 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 |
| vg0301154581 | NA | 2.29E-24 | mr1024_2 | 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 |
| vg0301154581 | NA | 4.90E-10 | mr1349_2 | 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 |
| vg0301154581 | NA | 6.36E-07 | mr1567_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 |
| vg0301154581 | NA | 4.15E-13 | mr1666_2 | 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 |
| vg0301154581 | NA | 3.44E-08 | mr1940_2 | 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 |