| Variant ID: vg1124774058 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 24774058 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CACAGCAACAGAGGTCTCTTTATTATAGAGTATAGGTACAGTCATGTTGGGCTGCGGACAGATCCCGAGCTCACAACTGCATTACAAAAGGGAAACGGAA[A/G]
CCAGGACTTGGACCAAACAACACAGGCGCGACTTGGGAACTAGGCCGAAACCCTCAAACTCATCGTAGCCGGCTTGCTCCTGGAAGAACTCCTCATCAGC
GCTGATGAGGAGTTCTTCCAGGAGCAAGCCGGCTACGATGAGTTTGAGGGTTTCGGCCTAGTTCCCAAGTCGCGCCTGTGTTGTTTGGTCCAAGTCCTGG[T/C]
TTCCGTTTCCCTTTTGTAATGCAGTTGTGAGCTCGGGATCTGTCCGCAGCCCAACATGACTGTACCTATACTCTATAATAAAGAGACCTCTGTTGCTGTG
| 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 | 16.80% | 10.80% | 2.54% | 69.89% | NA |
| All Indica | 2759 | 2.30% | 2.80% | 1.88% | 92.97% | NA |
| All Japonica | 1512 | 46.70% | 12.50% | 1.85% | 38.96% | NA |
| Aus | 269 | 3.30% | 80.30% | 9.29% | 7.06% | NA |
| Indica I | 595 | 1.20% | 2.90% | 1.01% | 94.96% | NA |
| Indica II | 465 | 0.40% | 0.60% | 0.86% | 98.06% | NA |
| Indica III | 913 | 3.10% | 3.30% | 2.74% | 90.91% | NA |
| Indica Intermediate | 786 | 3.40% | 3.60% | 2.16% | 90.84% | NA |
| Temperate Japonica | 767 | 76.30% | 4.80% | 0.78% | 18.12% | NA |
| Tropical Japonica | 504 | 5.80% | 24.00% | 1.98% | 68.25% | NA |
| Japonica Intermediate | 241 | 38.20% | 12.90% | 4.98% | 43.98% | NA |
| VI/Aromatic | 96 | 5.20% | 18.80% | 9.38% | 66.67% | NA |
| Intermediate | 90 | 11.10% | 8.90% | 6.67% | 73.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1124774058 | A -> DEL | N | N | silent_mutation | Average:20.253; most accessible tissue: Callus, score: 38.348 | N | N | N | N |
| vg1124774058 | A -> G | LOC_Os11g41310-LOC_Os11g41320 | intergenic_region ; MODIFIER | silent_mutation | Average:20.253; most accessible tissue: Callus, score: 38.348 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1124774058 | NA | 4.49E-06 | mr1179 | 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 |
| vg1124774058 | 2.16E-06 | 2.16E-06 | mr1609_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 |
| vg1124774058 | NA | 8.44E-10 | mr1916_2 | 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 |