| Variant ID: vg0608694617 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 8694617 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.02, others allele: 0.00, population size: 241. )
CAATCCAATGTCATACACCAAATTATACTGTCAGAATCGGCTGCATCGGCTCACCTAGTCCGACTCAGACCCAGCCGATCCTAATCGTAGCCGATCTGGA[C/T]
TTCAGCCGATTCTTGCTCTGTTCTCGGATCAATCTCCGCCTTCGACTCCACCTTGACCTAATCTCCTTTTCCGATGCTAATATTTCCAAATTTGGTCGTT
AACGACCAAATTTGGAAATATTAGCATCGGAAAAGGAGATTAGGTCAAGGTGGAGTCGAAGGCGGAGATTGATCCGAGAACAGAGCAAGAATCGGCTGAA[G/A]
TCCAGATCGGCTACGATTAGGATCGGCTGGGTCTGAGTCGGACTAGGTGAGCCGATGCAGCCGATTCTGACAGTATAATTTGGTGTATGACATTGGATTG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 43.10% | 21.40% | 0.53% | 34.96% | NA |
| All Indica | 2759 | 5.80% | 35.00% | 0.87% | 58.35% | NA |
| All Japonica | 1512 | 99.00% | 0.10% | 0.00% | 0.86% | NA |
| Aus | 269 | 85.50% | 13.80% | 0.37% | 0.37% | NA |
| Indica I | 595 | 4.50% | 40.30% | 0.34% | 54.79% | NA |
| Indica II | 465 | 5.80% | 16.10% | 1.08% | 76.99% | NA |
| Indica III | 913 | 4.20% | 50.20% | 0.88% | 44.80% | NA |
| Indica Intermediate | 786 | 8.70% | 24.40% | 1.15% | 65.78% | NA |
| Temperate Japonica | 767 | 99.10% | 0.00% | 0.00% | 0.91% | NA |
| Tropical Japonica | 504 | 99.20% | 0.20% | 0.00% | 0.60% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.40% | 0.00% | 1.24% | NA |
| VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 61.10% | 7.80% | 0.00% | 31.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0608694617 | C -> T | LOC_Os06g15310.1 | upstream_gene_variant ; 4572.0bp to feature; MODIFIER | silent_mutation | Average:31.469; most accessible tissue: Minghui63 flag leaf, score: 59.912 | N | N | N | N |
| vg0608694617 | C -> T | LOC_Os06g15320.1 | downstream_gene_variant ; 1096.0bp to feature; MODIFIER | silent_mutation | Average:31.469; most accessible tissue: Minghui63 flag leaf, score: 59.912 | N | N | N | N |
| vg0608694617 | C -> T | LOC_Os06g15310-LOC_Os06g15320 | intergenic_region ; MODIFIER | silent_mutation | Average:31.469; most accessible tissue: Minghui63 flag leaf, score: 59.912 | N | N | N | N |
| vg0608694617 | C -> DEL | N | N | silent_mutation | Average:31.469; most accessible tissue: Minghui63 flag leaf, score: 59.912 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0608694617 | NA | 4.60E-07 | mr1328 | Ind_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 |
| vg0608694617 | NA | 2.73E-06 | mr1446 | Ind_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 |
| vg0608694617 | NA | 1.96E-07 | mr1570 | Ind_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 |
| vg0608694617 | NA | 1.16E-06 | mr1570_2 | Ind_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 |