| Variant ID: vg1206196271 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 6196271 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CCGACGAAGTGGGAGGTGTTTCGACGAACTTCATCATGCATCATCTGGCGGTCAAGCCGGATGCCAAGCCAAGGGAACAGAAGCTGCACAAAATGTCCAC[C/T]
GATCACCAAGAGGCAGCAAAGCCCGAAGTGTAGAAGCTGCTCAAGGCTGGGGTGATCTAAGAGATCGACCACCCAGAGTGGTTGGCGAACCCATTTTTGG
CCAAAAATGGGTTCGCCAACCACTCTGGGTGGTCGATCTCTTAGATCACCCCAGCCTTGAGCAGCTTCTACACTTCGGGCTTTGCTGCCTCTTGGTGATC[G/A]
GTGGACATTTTGTGCAGCTTCTGTTCCCTTGGCTTGGCATCCGGCTTGACCGCCAGATGATGCATGATGAAGTTCGTCGAAACACCTCCCACTTCGTCGG
| 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 | 69.60% | 4.30% | 3.41% | 22.75% | NA |
| All Indica | 2759 | 86.30% | 0.60% | 1.09% | 11.96% | NA |
| All Japonica | 1512 | 38.50% | 11.80% | 6.35% | 43.39% | NA |
| Aus | 269 | 63.90% | 0.40% | 9.29% | 26.39% | NA |
| Indica I | 595 | 85.50% | 0.70% | 1.18% | 12.61% | NA |
| Indica II | 465 | 90.30% | 0.40% | 1.08% | 8.17% | NA |
| Indica III | 913 | 86.30% | 0.70% | 0.55% | 12.49% | NA |
| Indica Intermediate | 786 | 84.60% | 0.60% | 1.65% | 13.10% | NA |
| Temperate Japonica | 767 | 48.50% | 13.80% | 3.39% | 34.29% | NA |
| Tropical Japonica | 504 | 19.20% | 11.90% | 9.13% | 59.72% | NA |
| Japonica Intermediate | 241 | 46.90% | 5.00% | 9.96% | 38.17% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 65.60% | 5.60% | 11.11% | 17.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1206196271 | C -> DEL | N | N | silent_mutation | Average:8.667; most accessible tissue: Callus, score: 28.282 | N | N | N | N |
| vg1206196271 | C -> T | LOC_Os12g11450.1 | upstream_gene_variant ; 2689.0bp to feature; MODIFIER | silent_mutation | Average:8.667; most accessible tissue: Callus, score: 28.282 | N | N | N | N |
| vg1206196271 | C -> T | LOC_Os12g11470.1 | upstream_gene_variant ; 1384.0bp to feature; MODIFIER | silent_mutation | Average:8.667; most accessible tissue: Callus, score: 28.282 | N | N | N | N |
| vg1206196271 | C -> T | LOC_Os12g11460.1 | downstream_gene_variant ; 784.0bp to feature; MODIFIER | silent_mutation | Average:8.667; most accessible tissue: Callus, score: 28.282 | N | N | N | N |
| vg1206196271 | C -> T | LOC_Os12g11460-LOC_Os12g11470 | intergenic_region ; MODIFIER | silent_mutation | Average:8.667; most accessible tissue: Callus, score: 28.282 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1206196271 | 7.63E-06 | NA | mr1128_2 | 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 |
| vg1206196271 | NA | 7.97E-07 | mr1153_2 | 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 |
| vg1206196271 | 2.56E-06 | NA | mr1252_2 | 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 |
| vg1206196271 | NA | 6.77E-06 | mr1262_2 | 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 |