| Variant ID: vg1008686103 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 8686103 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 304. )
ACGGACAAAAAGTTATCGGATGTCAAGTTTGTATTCAATCCATACAACAAGAGGGCGGCAATACAATTAGCCCCAATACGATGGCAAAACATCATTAGTT[C/T]
ACTGTGTTCAGTTCAATAGTAATAGTATAACTATAAGTGATGGCAAAACATCATTAGTTCACTGCGTTCAGTTCAATAGTAATAGTATAACTATAAGTAA
TTACTTATAGTTATACTATTACTATTGAACTGAACGCAGTGAACTAATGATGTTTTGCCATCACTTATAGTTATACTATTACTATTGAACTGAACACAGT[G/A]
AACTAATGATGTTTTGCCATCGTATTGGGGCTAATTGTATTGCCGCCCTCTTGTTGTATGGATTGAATACAAACTTGACATCCGATAACTTTTTGTCCGT
| 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 | 91.10% | 6.10% | 1.40% | 1.44% | NA |
| All Indica | 2759 | 84.90% | 10.30% | 2.32% | 2.46% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.17% | 0.00% | NA |
| Indica II | 465 | 93.10% | 5.80% | 0.65% | 0.43% | NA |
| Indica III | 913 | 67.70% | 22.00% | 4.49% | 5.81% | NA |
| Indica Intermediate | 786 | 88.80% | 7.10% | 2.42% | 1.65% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 2.20% | 2.22% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1008686103 | C -> T | LOC_Os10g17270.1 | upstream_gene_variant ; 811.0bp to feature; MODIFIER | silent_mutation | Average:49.889; most accessible tissue: Zhenshan97 flag leaf, score: 70.837 | N | N | N | N |
| vg1008686103 | C -> T | LOC_Os10g17260.1 | downstream_gene_variant ; 4819.0bp to feature; MODIFIER | silent_mutation | Average:49.889; most accessible tissue: Zhenshan97 flag leaf, score: 70.837 | N | N | N | N |
| vg1008686103 | C -> T | LOC_Os10g17270-LOC_Os10g17280 | intergenic_region ; MODIFIER | silent_mutation | Average:49.889; most accessible tissue: Zhenshan97 flag leaf, score: 70.837 | N | N | N | N |
| vg1008686103 | C -> DEL | N | N | silent_mutation | Average:49.889; most accessible tissue: Zhenshan97 flag leaf, score: 70.837 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1008686103 | NA | 9.91E-06 | mr1113 | 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 |
| vg1008686103 | NA | 5.92E-06 | mr1247 | 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 |
| vg1008686103 | 3.88E-06 | NA | mr1720 | 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 |