| Variant ID: vg0432430016 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 32430016 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ATCCAATAATCTTAGAAATTCAATATCTTCCCAACCGTAAATCCGATTGACTCCGTTCAACTCCCAAAATTCCTCAAATCCCGAGATCTATCTAATGGCA[C/T]
GCTTAGAGGTCATTAATAAGGCTTTATTTTCGCCGTTTGTTGAGTTGTCCCGTTTTGCGTGTAGTTTCGGAGCCCGAAGACCCGCAGTGCGAGGATTTCG
CGAAATCCTCGCACTGCGGGTCTTCGGGCTCCGAAACTACACGCAAAACGGGACAACTCAACAAACGGCGAAAATAAAGCCTTATTAATGACCTCTAAGC[G/A]
TGCCATTAGATAGATCTCGGGATTTGAGGAATTTTGGGAGTTGAACGGAGTCAATCGGATTTACGGTTGGGAAGATATTGAATTTCTAAGATTATTGGAT
| 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 | 76.30% | 4.20% | 8.99% | 10.52% | NA |
| All Indica | 2759 | 76.50% | 0.10% | 12.29% | 11.05% | NA |
| All Japonica | 1512 | 83.00% | 11.80% | 3.31% | 1.92% | NA |
| Aus | 269 | 44.20% | 0.00% | 6.32% | 49.44% | NA |
| Indica I | 595 | 92.10% | 0.20% | 3.03% | 4.71% | NA |
| Indica II | 465 | 77.60% | 0.20% | 12.04% | 10.11% | NA |
| Indica III | 913 | 60.80% | 0.10% | 21.91% | 17.20% | NA |
| Indica Intermediate | 786 | 82.30% | 0.10% | 8.27% | 9.29% | NA |
| Temperate Japonica | 767 | 96.60% | 3.30% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 78.20% | 7.10% | 8.93% | 5.75% | NA |
| Japonica Intermediate | 241 | 49.80% | 48.50% | 1.66% | 0.00% | NA |
| VI/Aromatic | 96 | 49.00% | 10.40% | 15.62% | 25.00% | NA |
| Intermediate | 90 | 82.20% | 6.70% | 4.44% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0432430016 | C -> DEL | N | N | silent_mutation | Average:19.733; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |
| vg0432430016 | C -> T | LOC_Os04g54510.1 | upstream_gene_variant ; 4398.0bp to feature; MODIFIER | silent_mutation | Average:19.733; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |
| vg0432430016 | C -> T | LOC_Os04g54520.1 | downstream_gene_variant ; 13.0bp to feature; MODIFIER | silent_mutation | Average:19.733; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |
| vg0432430016 | C -> T | LOC_Os04g54510-LOC_Os04g54520 | intergenic_region ; MODIFIER | silent_mutation | Average:19.733; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0432430016 | NA | 2.01E-06 | mr1691_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 |
| vg0432430016 | 4.64E-06 | NA | mr1733_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 |
| vg0432430016 | 8.40E-07 | NA | mr1946_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 |
| vg0432430016 | 8.40E-07 | NA | mr1948_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 |