| Variant ID: vg0139341179 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 39341179 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TCCCGAGTTTCTCTGAAACCGAGTGGCCTTGGAGGAGATTGGCGGCTGCCGTGCCTGAGGAAGACGACGACGACGCCATGTGGATGAAAGATGCGATCTA[T/C]
CGAGGTGGAAAAAGGATCTGATACCATGTGATAAAATGTGAAGCGTTGAACCCTTTGCCTCGGGCCGCATCTCTGTTAAATAGTGGTAGAAACAGCCTCT
AGAGGCTGTTTCTACCACTATTTAACAGAGATGCGGCCCGAGGCAAAGGGTTCAACGCTTCACATTTTATCACATGGTATCAGATCCTTTTTCCACCTCG[A/G]
TAGATCGCATCTTTCATCCACATGGCGTCGTCGTCGTCTTCCTCAGGCACGGCAGCCGCCAATCTCCTCCAAGGCCACTCGGTTTCAGAGAAACTCGGGA
| 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 | 34.30% | 26.20% | 7.64% | 31.93% | NA |
| All Indica | 2759 | 4.30% | 33.60% | 12.11% | 49.91% | NA |
| All Japonica | 1512 | 93.30% | 2.10% | 0.93% | 3.77% | NA |
| Aus | 269 | 3.00% | 93.70% | 1.12% | 2.23% | NA |
| Indica I | 595 | 4.00% | 30.10% | 18.15% | 47.73% | NA |
| Indica II | 465 | 4.70% | 4.10% | 9.46% | 81.72% | NA |
| Indica III | 913 | 2.20% | 50.90% | 9.64% | 37.24% | NA |
| Indica Intermediate | 786 | 6.90% | 33.70% | 11.96% | 47.46% | NA |
| Temperate Japonica | 767 | 98.70% | 0.10% | 0.13% | 1.04% | NA |
| Tropical Japonica | 504 | 85.90% | 5.40% | 1.79% | 6.94% | NA |
| Japonica Intermediate | 241 | 91.30% | 1.20% | 1.66% | 5.81% | NA |
| VI/Aromatic | 96 | 33.30% | 13.50% | 4.17% | 48.96% | NA |
| Intermediate | 90 | 54.40% | 14.40% | 6.67% | 24.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0139341179 | T -> DEL | N | N | silent_mutation | Average:8.964; most accessible tissue: Callus, score: 42.343 | N | N | N | N |
| vg0139341179 | T -> C | LOC_Os01g67690.1 | upstream_gene_variant ; 22.0bp to feature; MODIFIER | silent_mutation | Average:8.964; most accessible tissue: Callus, score: 42.343 | N | N | N | N |
| vg0139341179 | T -> C | LOC_Os01g67700.1 | upstream_gene_variant ; 4254.0bp to feature; MODIFIER | silent_mutation | Average:8.964; most accessible tissue: Callus, score: 42.343 | N | N | N | N |
| vg0139341179 | T -> C | LOC_Os01g67690-LOC_Os01g67700 | intergenic_region ; MODIFIER | silent_mutation | Average:8.964; most accessible tissue: Callus, score: 42.343 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0139341179 | NA | 2.92E-10 | Grain_weight | All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg0139341179 | 6.47E-06 | 8.49E-06 | mr1453 | 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 |
| vg0139341179 | NA | 2.19E-18 | mr1383_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 |