| Variant ID: vg0206503587 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 6503587 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
AATCAACACACAAAAAAGCAAAAGGCCAATATTTGTTCAGATAAAAAGTATTGTATCCACGATTGACCCTGCAACGGATGATCGACGGGCAAATCAAAGC[C/G]
AGGCGGCCAAATCAAGCGTCCTTCATCTTCTTGGTGGAGATGGATGGCTTGTCGGTGGGCTGAGGAGTCTGAACCATGGGTTATGAACCGAGAGATTGAA
TTCAATCTCTCGGTTCATAACCCATGGTTCAGACTCCTCAGCCCACCGACAAGCCATCCATCTCCACCAAGAAGATGAAGGACGCTTGATTTGGCCGCCT[G/C]
GCTTTGATTTGCCCGTCGATCATCCGTTGCAGGGTCAATCGTGGATACAATACTTTTTATCTGAACAAATATTGGCCTTTTGCTTTTTTGTGTGTTGATT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 72.20% | 2.30% | 3.43% | 22.09% | NA |
| All Indica | 2759 | 69.00% | 3.50% | 4.31% | 23.20% | NA |
| All Japonica | 1512 | 90.50% | 0.10% | 0.07% | 9.33% | NA |
| Aus | 269 | 8.20% | 2.20% | 11.90% | 77.70% | NA |
| Indica I | 595 | 71.10% | 0.70% | 1.85% | 26.39% | NA |
| Indica II | 465 | 67.70% | 1.30% | 4.09% | 26.88% | NA |
| Indica III | 913 | 70.00% | 6.50% | 5.59% | 17.96% | NA |
| Indica Intermediate | 786 | 67.00% | 3.40% | 4.83% | 24.68% | NA |
| Temperate Japonica | 767 | 95.00% | 0.00% | 0.13% | 4.82% | NA |
| Tropical Japonica | 504 | 94.40% | 0.20% | 0.00% | 5.36% | NA |
| Japonica Intermediate | 241 | 68.00% | 0.00% | 0.00% | 31.95% | NA |
| VI/Aromatic | 96 | 45.80% | 4.20% | 9.38% | 40.62% | NA |
| Intermediate | 90 | 78.90% | 3.30% | 1.11% | 16.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0206503587 | C -> G | LOC_Os02g12470.1 | intron_variant ; MODIFIER | silent_mutation | Average:26.143; most accessible tissue: Zhenshan97 panicle, score: 63.607 | N | N | N | N |
| vg0206503587 | C -> DEL | N | N | silent_mutation | Average:26.143; most accessible tissue: Zhenshan97 panicle, score: 63.607 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0206503587 | 2.32E-06 | NA | mr1158 | 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 |
| vg0206503587 | 7.51E-06 | NA | mr1383 | 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 |