| Variant ID: vg1219795565 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr12 | Position: 19795565 |
| Reference Allele: A | Alternative Allele: AGAGG |
| Primary Allele: A | Secondary Allele: AGAGG |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 277. )
GTAGAGCGGCTTCGGGCCTTGAGCCTTCTTGACATCGTTGAGAGGTGCATGGGAGCATGAGAGGGGGAGTGGGACAACACGTTAGACTAAAGATAGAGAG[A/AGAGG]
GAGAGGGAGAGGGAGAGGAGGAAGATAAGCTGGTGGATGAATCTCAAGATGATGCAAAAGTCCATTTGTAAGATGTTAAGCAACGTTTCCGTTAAATGTG
CACATTTAACGGAAACGTTGCTTAACATCTTACAAATGGACTTTTGCATCATCTTGAGATTCATCCACCAGCTTATCTTCCTCCTCTCCCTCTCCCTCTC[T/CCTCT]
CTCTCTATCTTTAGTCTAACGTGTTGTCCCACTCCCCCTCTCATGCTCCCATGCACCTCTCAACGATGTCAAGAAGGCTCAAGGCCCGAAGCCGCTCTAC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of AGAGG(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 95.70% | 0.50% | 0.23% | 3.53% | NA |
| All Indica | 2759 | 99.30% | 0.70% | 0.00% | 0.04% | NA |
| All Japonica | 1512 | 88.50% | 0.00% | 0.66% | 10.85% | NA |
| Aus | 269 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.90% | 0.90% | 0.00% | 0.22% | NA |
| Indica III | 913 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 82.70% | 0.00% | 0.65% | 16.69% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 83.40% | 0.00% | 2.07% | 14.52% | NA |
| VI/Aromatic | 96 | 97.90% | 1.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 96.70% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1219795565 | A -> DEL | N | N | silent_mutation | Average:55.593; most accessible tissue: Callus, score: 75.48 | N | N | N | N |
| vg1219795565 | A -> AGAGG | LOC_Os12g32760.1 | upstream_gene_variant ; 4083.0bp to feature; MODIFIER | silent_mutation | Average:55.593; most accessible tissue: Callus, score: 75.48 | N | N | N | N |
| vg1219795565 | A -> AGAGG | LOC_Os12g32770.1 | downstream_gene_variant ; 1475.0bp to feature; MODIFIER | silent_mutation | Average:55.593; most accessible tissue: Callus, score: 75.48 | N | N | N | N |
| vg1219795565 | A -> AGAGG | LOC_Os12g32770-LOC_Os12g32790 | intergenic_region ; MODIFIER | silent_mutation | Average:55.593; most accessible tissue: Callus, score: 75.48 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1219795565 | 5.53E-07 | 5.53E-07 | mr1343 | 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 |
| vg1219795565 | NA | 2.40E-06 | mr1038_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 |
| vg1219795565 | NA | 2.96E-06 | mr1354_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 |