| Variant ID: vg0421045958 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 21045958 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CACTCACTTAGTTGATTTTTTTTAAAAGAGTTCAAATAAAATAAATTGCAAAAACAACAGTCCTTCCCTTGAAGCCTGCATTAAACACTATTTCCCATGG[C/T]
TTGCTGAGTACTCCTGTACTCACCCTTGCTCTATATAAATAATCCCCCCCAGTTGCTGAAGAAGATGAAGCGGATCTCGCTGACGAGGAGTTTTTCCAGG
CCTGGAAAAACTCCTCGTCAGCGAGATCCGCTTCATCTTCTTCAGCAACTGGGGGGGATTATTTATATAGAGCAAGGGTGAGTACAGGAGTACTCAGCAA[G/A]
CCATGGGAAATAGTGTTTAATGCAGGCTTCAAGGGAAGGACTGTTGTTTTTGCAATTTATTTTATTTGAACTCTTTTAAAAAAAATCAACTAAGTGAGTG
| 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 | 78.00% | 1.70% | 4.89% | 15.36% | NA |
| All Indica | 2759 | 67.30% | 0.00% | 7.39% | 25.30% | NA |
| All Japonica | 1512 | 92.70% | 5.20% | 1.12% | 0.93% | NA |
| Aus | 269 | 98.90% | 0.00% | 0.37% | 0.74% | NA |
| Indica I | 595 | 63.00% | 0.00% | 7.39% | 29.58% | NA |
| Indica II | 465 | 43.40% | 0.00% | 13.33% | 43.23% | NA |
| Indica III | 913 | 85.70% | 0.00% | 3.29% | 11.06% | NA |
| Indica Intermediate | 786 | 63.20% | 0.10% | 8.65% | 27.99% | NA |
| Temperate Japonica | 767 | 97.50% | 1.70% | 0.65% | 0.13% | NA |
| Tropical Japonica | 504 | 84.90% | 10.90% | 1.59% | 2.58% | NA |
| Japonica Intermediate | 241 | 93.80% | 4.60% | 1.66% | 0.00% | NA |
| VI/Aromatic | 96 | 88.50% | 0.00% | 7.29% | 4.17% | NA |
| Intermediate | 90 | 87.80% | 1.10% | 2.22% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0421045958 | C -> DEL | N | N | silent_mutation | Average:12.987; most accessible tissue: Callus, score: 26.397 | N | N | N | N |
| vg0421045958 | C -> T | LOC_Os04g34740.1 | upstream_gene_variant ; 2841.0bp to feature; MODIFIER | silent_mutation | Average:12.987; most accessible tissue: Callus, score: 26.397 | N | N | N | N |
| vg0421045958 | C -> T | LOC_Os04g34740-LOC_Os04g34750 | intergenic_region ; MODIFIER | silent_mutation | Average:12.987; most accessible tissue: Callus, score: 26.397 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0421045958 | 5.52E-06 | 5.52E-06 | mr1054 | 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 |
| vg0421045958 | NA | 2.14E-06 | mr1287 | 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 |
| vg0421045958 | 7.91E-06 | 7.91E-06 | mr1372 | 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 |
| vg0421045958 | 3.97E-06 | 3.97E-06 | mr1680 | 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 |
| vg0421045958 | NA | 7.78E-09 | mr1746 | 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 |
| vg0421045958 | NA | 7.22E-11 | mr1951 | 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 |