| Variant ID: vg0414572804 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 14572804 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CAACTGCATTACAAAAGGGAAACGGAAGCCAGGGCTTGGACCAAACATCACAGGCGCGACTTGGGAACTAGGCCGAAACCCTAAAACTCATCGAAGCCGG[C/T]
TTGCTCCTGGAAGAACTCCTCATCAGCGGGATCCGCTTCATCTTCTTCAGCAACTGGAGGGGGGAATTATTTATATAGAGCAAAGGTGAGTACAGGAGTA
TACTCCTGTACTCACCTTTGCTCTATATAAATAATTCCCCCCTCCAGTTGCTGAAGAAGATGAAGCGGATCCCGCTGATGAGGAGTTCTTCCAGGAGCAA[G/A]
CCGGCTTCGATGAGTTTTAGGGTTTCGGCCTAGTTCCCAAGTCGCGCCTGTGATGTTTGGTCCAAGCCCTGGCTTCCGTTTCCCTTTTGTAATGCAGTTG
| 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 | 81.80% | 0.20% | 3.07% | 14.94% | NA |
| All Indica | 2759 | 78.60% | 0.10% | 1.78% | 19.54% | NA |
| All Japonica | 1512 | 90.80% | 0.30% | 4.17% | 4.76% | NA |
| Aus | 269 | 66.50% | 0.00% | 2.97% | 30.48% | NA |
| Indica I | 595 | 71.30% | 0.20% | 2.35% | 26.22% | NA |
| Indica II | 465 | 65.60% | 0.00% | 2.58% | 31.83% | NA |
| Indica III | 913 | 91.80% | 0.00% | 0.66% | 7.56% | NA |
| Indica Intermediate | 786 | 76.60% | 0.10% | 2.16% | 21.12% | NA |
| Temperate Japonica | 767 | 89.30% | 0.10% | 4.95% | 5.61% | NA |
| Tropical Japonica | 504 | 93.70% | 0.00% | 1.98% | 4.37% | NA |
| Japonica Intermediate | 241 | 89.60% | 1.20% | 6.22% | 2.90% | NA |
| VI/Aromatic | 96 | 69.80% | 2.10% | 22.92% | 5.21% | NA |
| Intermediate | 90 | 86.70% | 1.10% | 3.33% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0414572804 | C -> DEL | N | N | silent_mutation | Average:5.36; most accessible tissue: Callus, score: 12.276 | N | N | N | N |
| vg0414572804 | C -> T | LOC_Os04g25210.1 | downstream_gene_variant ; 3712.0bp to feature; MODIFIER | silent_mutation | Average:5.36; most accessible tissue: Callus, score: 12.276 | N | N | N | N |
| vg0414572804 | C -> T | LOC_Os04g25190-LOC_Os04g25210 | intergenic_region ; MODIFIER | silent_mutation | Average:5.36; most accessible tissue: Callus, score: 12.276 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0414572804 | 5.85E-06 | 4.08E-07 | mr1827_2 | 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 |
| vg0414572804 | 4.00E-07 | 5.41E-08 | mr1842_2 | 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 |
| vg0414572804 | 2.10E-06 | 2.10E-06 | mr1933_2 | 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 |