| Variant ID: vg0717031754 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 17031754 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
ATGACCAAAATAAAAGTTTTAGATCTTGATGAGTTATTCAACTTTGTTGTTGATAACTTTTTCAGTTGATATCATTTAGTATTTGAAAATATTGTTTGAA[A/G]
TTGTCATATTTTTAAATTCAAATTCAAACAGTTCAAAAAATGTTATATAGAAAAATGACCAAAATAAAAGTTATAGATTTTGATGAGTTATACAACTTTG
CAAAGTTGTATAACTCATCAAAATCTATAACTTTTATTTTGGTCATTTTTCTATATAACATTTTTTGAACTGTTTGAATTTGAATTTAAAAATATGACAA[T/C]
TTCAAACAATATTTTCAAATACTAAATGATATCAACTGAAAAAGTTATCAACAACAAAGTTGAATAACTCATCAAGATCTAAAACTTTTATTTTGGTCAT
| 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 | 33.80% | 2.90% | 1.71% | 61.55% | NA |
| All Indica | 2759 | 4.60% | 0.40% | 1.99% | 92.93% | NA |
| All Japonica | 1512 | 86.50% | 7.50% | 0.73% | 5.29% | NA |
| Aus | 269 | 8.20% | 3.70% | 4.83% | 83.27% | NA |
| Indica I | 595 | 4.40% | 0.00% | 3.03% | 92.61% | NA |
| Indica II | 465 | 3.70% | 0.60% | 0.86% | 94.84% | NA |
| Indica III | 913 | 2.50% | 0.20% | 1.10% | 96.17% | NA |
| Indica Intermediate | 786 | 7.90% | 0.90% | 2.93% | 88.30% | NA |
| Temperate Japonica | 767 | 79.70% | 12.50% | 1.43% | 6.39% | NA |
| Tropical Japonica | 504 | 94.40% | 1.80% | 0.00% | 3.77% | NA |
| Japonica Intermediate | 241 | 91.70% | 3.30% | 0.00% | 4.98% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 1.04% | 3.12% | NA |
| Intermediate | 90 | 54.40% | 2.20% | 1.11% | 42.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0717031754 | A -> DEL | N | N | silent_mutation | Average:6.428; most accessible tissue: Callus, score: 17.926 | N | N | N | N |
| vg0717031754 | A -> G | LOC_Os07g29030.1 | downstream_gene_variant ; 4717.0bp to feature; MODIFIER | silent_mutation | Average:6.428; most accessible tissue: Callus, score: 17.926 | N | N | N | N |
| vg0717031754 | A -> G | LOC_Os07g29040.1 | downstream_gene_variant ; 2523.0bp to feature; MODIFIER | silent_mutation | Average:6.428; most accessible tissue: Callus, score: 17.926 | N | N | N | N |
| vg0717031754 | A -> G | LOC_Os07g29050.1 | intron_variant ; MODIFIER | silent_mutation | Average:6.428; most accessible tissue: Callus, score: 17.926 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0717031754 | NA | 3.05E-07 | mr1915 | 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 |
| vg0717031754 | NA | 1.02E-12 | mr1325_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 |
| vg0717031754 | NA | 3.67E-14 | mr1326_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 |
| vg0717031754 | 6.31E-07 | 6.31E-07 | mr1514_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 |
| vg0717031754 | NA | 5.69E-09 | mr1690_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 |