| Variant ID: vg0429645134 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 29645134 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TCACTCTCTCCTTCCCCTTCCCTCTCTCCCCGTTCTCTCTCTTTATCTCTGTCACACCCTGAAGTTCTCCTCCTAAGTCTAAAATTGAATTTATAAATCA[C/T]
CCTAAGAAAATGCCGGTGCAAATCAAGAGAAAACCTTAATAAATTAATGCAAATAATAATCGAAATTGGCATGTGGAATTTTTTTTTTGAGTTCTACATG
CATGTAGAACTCAAAAAAAAAATTCCACATGCCAATTTCGATTATTATTTGCATTAATTTATTAAGGTTTTCTCTTGATTTGCACCGGCATTTTCTTAGG[G/A]
TGATTTATAAATTCAATTTTAGACTTAGGAGGAGAACTTCAGGGTGTGACAGAGATAAAGAGAGAGAACGGGGAGAGAGGGAAGGGGAAGGAGAGAGTGA
| 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 | 85.20% | 13.10% | 1.71% | 0.00% | NA |
| All Indica | 2759 | 96.80% | 1.30% | 1.88% | 0.00% | NA |
| All Japonica | 1512 | 60.70% | 37.60% | 1.72% | 0.00% | NA |
| Aus | 269 | 99.30% | 0.00% | 0.74% | 0.00% | NA |
| Indica I | 595 | 98.00% | 1.80% | 0.17% | 0.00% | NA |
| Indica II | 465 | 98.90% | 0.60% | 0.43% | 0.00% | NA |
| Indica III | 913 | 96.70% | 0.30% | 2.96% | 0.00% | NA |
| Indica Intermediate | 786 | 94.80% | 2.40% | 2.80% | 0.00% | NA |
| Temperate Japonica | 767 | 32.90% | 64.40% | 2.74% | 0.00% | NA |
| Tropical Japonica | 504 | 93.30% | 6.50% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 81.30% | 17.00% | 1.66% | 0.00% | NA |
| VI/Aromatic | 96 | 90.60% | 9.40% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 5.60% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0429645134 | C -> T | LOC_Os04g49700.1 | downstream_gene_variant ; 2572.0bp to feature; MODIFIER | silent_mutation | Average:27.758; most accessible tissue: Minghui63 panicle, score: 53.77 | N | N | N | N |
| vg0429645134 | C -> T | LOC_Os04g49700-LOC_Os04g49710 | intergenic_region ; MODIFIER | silent_mutation | Average:27.758; most accessible tissue: Minghui63 panicle, score: 53.77 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0429645134 | 1.52E-07 | NA | mr1549_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 |
| vg0429645134 | 7.97E-06 | NA | mr1757_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 |