| Variant ID: vg0613618219 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 13618219 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
ATAGGATATCTTCTCTGGCGGCTCTCTTAAGCTCACGCCAGTGAAGGTATTGTATCTTTGCTGGCGGTAAGGGGATGCGGCCCGCCAGCGAAGATATAGG[C/T]
GTCTTCGCTGGCGGCCCTCTTAACTTAACGCCAGCGAAGATACCATATCTTCGCTGGCAGTGTGATGACGTGGACCGCCAGCGAAGATACCTGCATCTTC
GAAGATGCAGGTATCTTCGCTGGCGGTCCACGTCATCACACTGCCAGCGAAGATATGGTATCTTCGCTGGCGTTAAGTTAAGAGGGCCGCCAGCGAAGAC[G/A]
CCTATATCTTCGCTGGCGGGCCGCATCCCCTTACCGCCAGCAAAGATACAATACCTTCACTGGCGTGAGCTTAAGAGAGCCGCCAGAGAAGATATCCTAT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 83.90% | 12.30% | 2.94% | 0.87% | NA |
| All Indica | 2759 | 97.00% | 0.30% | 1.34% | 1.41% | NA |
| All Japonica | 1512 | 56.30% | 37.30% | 6.28% | 0.07% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.37% | 0.00% | NA |
| Indica I | 595 | 95.60% | 0.50% | 2.69% | 1.18% | NA |
| Indica II | 465 | 91.00% | 0.20% | 3.01% | 5.81% | NA |
| Indica III | 913 | 99.90% | 0.00% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 98.10% | 0.50% | 0.76% | 0.64% | NA |
| Temperate Japonica | 767 | 22.70% | 67.00% | 10.17% | 0.13% | NA |
| Tropical Japonica | 504 | 94.60% | 4.20% | 1.19% | 0.00% | NA |
| Japonica Intermediate | 241 | 83.40% | 12.00% | 4.56% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 82.20% | 10.00% | 6.67% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0613618219 | C -> T | LOC_Os06g23320.1 | upstream_gene_variant ; 750.0bp to feature; MODIFIER | silent_mutation | Average:33.859; most accessible tissue: Callus, score: 52.461 | N | N | N | N |
| vg0613618219 | C -> T | LOC_Os06g23310.1 | downstream_gene_variant ; 1353.0bp to feature; MODIFIER | silent_mutation | Average:33.859; most accessible tissue: Callus, score: 52.461 | N | N | N | N |
| vg0613618219 | C -> T | LOC_Os06g23330.1 | downstream_gene_variant ; 4747.0bp to feature; MODIFIER | silent_mutation | Average:33.859; most accessible tissue: Callus, score: 52.461 | N | N | N | N |
| vg0613618219 | C -> T | LOC_Os06g23310-LOC_Os06g23320 | intergenic_region ; MODIFIER | silent_mutation | Average:33.859; most accessible tissue: Callus, score: 52.461 | N | N | N | N |
| vg0613618219 | C -> DEL | N | N | silent_mutation | Average:33.859; most accessible tissue: Callus, score: 52.461 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0613618219 | 1.17E-06 | NA | mr1672 | 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 |
| vg0613618219 | NA | 6.22E-10 | mr1570_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 |
| vg0613618219 | NA | 5.52E-06 | mr1617_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 |