| Variant ID: vg0809694186 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 9694186 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TCGCTTGCCAGATCAATCTAATCCGTTGAATCTTGGTCAACTCTATGTCAAGATTAATCTTAGTCGTCTAAAATCGATATAAATCCGTTCCCTCTTTTCA[A/G]
TGGCATATTATTTCTTTTTAATATATGTCATCTACCAAATATAATCTAATCTATTTCCGGAGGTTGTTTTTATCTTAGTTATAAATCATTTGTAAATGGT
ACCATTTACAAATGATTTATAACTAAGATAAAAACAACCTCCGGAAATAGATTAGATTATATTTGGTAGATGACATATATTAAAAAGAAATAATATGCCA[T/C]
TGAAAAGAGGGAACGGATTTATATCGATTTTAGACGACTAAGATTAATCTTGACATAGAGTTGACCAAGATTCAACGGATTAGATTGATCTGGCAAGCGA
| 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 | 83.70% | 2.70% | 10.58% | 3.03% | NA |
| All Indica | 2759 | 89.50% | 0.90% | 9.35% | 0.25% | NA |
| All Japonica | 1512 | 77.40% | 6.60% | 7.08% | 8.86% | NA |
| Aus | 269 | 75.50% | 0.00% | 24.54% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 65.60% | 3.70% | 30.11% | 0.65% | NA |
| Indica III | 913 | 93.10% | 0.30% | 6.24% | 0.33% | NA |
| Indica Intermediate | 786 | 91.50% | 0.60% | 7.76% | 0.13% | NA |
| Temperate Japonica | 767 | 95.80% | 0.00% | 2.09% | 2.09% | NA |
| Tropical Japonica | 504 | 49.40% | 17.90% | 13.29% | 19.44% | NA |
| Japonica Intermediate | 241 | 77.60% | 4.10% | 9.96% | 8.30% | NA |
| VI/Aromatic | 96 | 34.40% | 2.10% | 62.50% | 1.04% | NA |
| Intermediate | 90 | 87.80% | 1.10% | 10.00% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0809694186 | A -> G | LOC_Os08g15900.1 | downstream_gene_variant ; 4173.0bp to feature; MODIFIER | silent_mutation | Average:33.053; most accessible tissue: Zhenshan97 flag leaf, score: 62.519 | N | N | N | N |
| vg0809694186 | A -> G | LOC_Os08g15910.1 | downstream_gene_variant ; 1645.0bp to feature; MODIFIER | silent_mutation | Average:33.053; most accessible tissue: Zhenshan97 flag leaf, score: 62.519 | N | N | N | N |
| vg0809694186 | A -> G | LOC_Os08g15920.1 | intron_variant ; MODIFIER | silent_mutation | Average:33.053; most accessible tissue: Zhenshan97 flag leaf, score: 62.519 | N | N | N | N |
| vg0809694186 | A -> DEL | N | N | silent_mutation | Average:33.053; most accessible tissue: Zhenshan97 flag leaf, score: 62.519 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0809694186 | 9.21E-08 | NA | mr1301_2 | 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 |