| Variant ID: vg0612563711 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 12563711 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AAACTTTCTGTTGTTCTGCCACCCAAGTAAACTGATGATCGGCCTTCAATCTCATTAATGGTGTAAAAGGCTCTAACCTTCCAGACAAATTAGAAATAAA[T/C]
CTTCAAACAAAATTAATTTTGCCGATCATCTCCTGCAATTCTGTCTTGTTCTCTGGAGGCTTAATCTTCTTGATCGCATTGACACTTCTTTGAGTTATTT
AAATAACTCAAAGAAGTGTCAATGCGATCAAGAAGATTAAGCCTCCAGAGAACAAGACAGAATTGCAGGAGATGATCGGCAAAATTAATTTTGTTTGAAG[A/G]
TTTATTTCTAATTTGTCTGGAAGGTTAGAGCCTTTTACACCATTAATGAGATTGAAGGCCGATCATCAGTTTACTTGGGTGGCAGAACAACAGAAAGTTT
| 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 | 37.50% | 34.60% | 13.48% | 14.49% | NA |
| All Indica | 2759 | 54.30% | 5.40% | 21.35% | 18.88% | NA |
| All Japonica | 1512 | 0.70% | 89.00% | 0.86% | 9.46% | NA |
| Aus | 269 | 75.80% | 16.40% | 7.81% | 0.00% | NA |
| Indica I | 595 | 23.40% | 8.90% | 35.29% | 32.44% | NA |
| Indica II | 465 | 45.60% | 5.40% | 23.66% | 25.38% | NA |
| Indica III | 913 | 81.50% | 1.30% | 9.42% | 7.78% | NA |
| Indica Intermediate | 786 | 51.40% | 7.60% | 23.28% | 17.68% | NA |
| Temperate Japonica | 767 | 0.10% | 97.00% | 0.39% | 2.48% | NA |
| Tropical Japonica | 504 | 1.60% | 76.40% | 1.19% | 20.83% | NA |
| Japonica Intermediate | 241 | 0.80% | 89.60% | 1.66% | 7.88% | NA |
| VI/Aromatic | 96 | 30.20% | 58.30% | 4.17% | 7.29% | NA |
| Intermediate | 90 | 31.10% | 42.20% | 11.11% | 15.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0612563711 | T -> C | LOC_Os06g21730.1 | downstream_gene_variant ; 2655.0bp to feature; MODIFIER | silent_mutation | Average:17.933; most accessible tissue: Callus, score: 32.816 | N | N | N | N |
| vg0612563711 | T -> C | LOC_Os06g21740.1 | intron_variant ; MODIFIER | silent_mutation | Average:17.933; most accessible tissue: Callus, score: 32.816 | N | N | N | N |
| vg0612563711 | T -> DEL | N | N | silent_mutation | Average:17.933; most accessible tissue: Callus, score: 32.816 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0612563711 | 4.66E-07 | NA | mr1017 | 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 |
| vg0612563711 | 3.64E-06 | NA | mr1055 | 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 |
| vg0612563711 | 4.89E-07 | NA | mr1132 | 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 |
| vg0612563711 | 2.06E-06 | NA | mr1390 | 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 |
| vg0612563711 | 5.72E-06 | NA | mr1490 | 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 |