| Variant ID: vg0210480404 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 10480404 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TGAAGGAGACTCTCAAGAAGGCTTTTGATCAAGTCTACGCCGCATTTGAGCCGCTAAGCGATGTAGATGGTGATAGTGGCGATGAAGATAAGGGAAAGAA[C/T]
ATCTCCGGTGTTTGCTTCATGGCGCGTGGTGAATCGGATTCATAGTGTGAAGACAATGAAGTACGTGTTTTTGAGGAAGCTATTCTTATTTTAAGTGAGA
TCTCACTTAAAATAAGAATAGCTTCCTCAAAAACACGTACTTCATTGTCTTCACACTATGAATCCGATTCACCACGCGCCATGAAGCAAACACCGGAGAT[G/A]
TTCTTTCCCTTATCTTCATCGCCACTATCACCATCTACATCGCTTAGCGGCTCAAATGCGGCGTAGACTTGATCAAAAGCCTTCTTGAGAGTCTCCTTCA
| 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 | 87.70% | 0.50% | 6.47% | 5.29% | NA |
| All Indica | 2759 | 82.20% | 0.90% | 9.82% | 7.10% | NA |
| All Japonica | 1512 | 99.50% | 0.00% | 0.20% | 0.26% | NA |
| Aus | 269 | 73.20% | 0.40% | 9.29% | 17.10% | NA |
| Indica I | 595 | 74.80% | 0.70% | 13.78% | 10.76% | NA |
| Indica II | 465 | 82.60% | 0.90% | 9.03% | 7.53% | NA |
| Indica III | 913 | 87.40% | 1.10% | 7.78% | 3.72% | NA |
| Indica Intermediate | 786 | 81.60% | 0.80% | 9.67% | 8.02% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.13% | 0.26% | NA |
| Tropical Japonica | 504 | 99.40% | 0.00% | 0.20% | 0.40% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 87.80% | 0.00% | 7.78% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0210480404 | C -> T | LOC_Os02g18050.1 | synonymous_variant ; p.Asn108Asn; LOW | synonymous_codon | Average:22.026; most accessible tissue: Zhenshan97 root, score: 39.742 | N | N | N | N |
| vg0210480404 | C -> DEL | LOC_Os02g18050.1 | N | frameshift_variant | Average:22.026; most accessible tissue: Zhenshan97 root, score: 39.742 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0210480404 | NA | 2.73E-07 | mr1129_2 | Ind_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 |
| vg0210480404 | 5.80E-07 | NA | mr1255_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 |
| vg0210480404 | 1.18E-06 | 4.42E-08 | mr1255_2 | Ind_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 |