| Variant ID: vg0620619372 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 20619372 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CCTCACGTTTCGTGCATCTTCGCCGAAGTCTTTAAATGTTCTGTTGATATTTCGCCACTGCGACCCGTCAGCGGGGTGTCTCAGCATCCCATCCTATTTA[C/T]
GTTCTTCTGCGTGCCACCGCATCATTCTAGCATGTGATTTGTTCCTGAAAAACCGCTTCAGCCTTGGTATTATAGGGAAATACCACATCACTTTAGCAGG
CCTGCTAAAGTGATGTGGTATTTCCCTATAATACCAAGGCTGAAGCGGTTTTTCAGGAACAAATCACATGCTAGAATGATGCGGTGGCACGCAGAAGAAC[G/A]
TAAATAGGATGGGATGCTGAGACACCCCGCTGACGGGTCGCAGTGGCGAAATATCAACAGAACATTTAAAGACTTCGGCGAAGATGCACGAAACGTGAGG
| 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 | 84.40% | 2.90% | 7.30% | 5.40% | NA |
| All Indica | 2759 | 81.00% | 4.70% | 7.32% | 6.96% | NA |
| All Japonica | 1512 | 97.80% | 0.10% | 0.26% | 1.85% | NA |
| Aus | 269 | 43.90% | 0.00% | 46.47% | 9.67% | NA |
| Indica I | 595 | 92.40% | 0.20% | 3.53% | 3.87% | NA |
| Indica II | 465 | 69.20% | 14.20% | 10.11% | 6.45% | NA |
| Indica III | 913 | 82.40% | 0.90% | 8.00% | 8.76% | NA |
| Indica Intermediate | 786 | 77.90% | 6.90% | 7.76% | 7.51% | NA |
| Temperate Japonica | 767 | 98.30% | 0.10% | 0.13% | 1.43% | NA |
| Tropical Japonica | 504 | 97.40% | 0.20% | 0.60% | 1.79% | NA |
| Japonica Intermediate | 241 | 96.70% | 0.00% | 0.00% | 3.32% | NA |
| VI/Aromatic | 96 | 86.50% | 0.00% | 9.38% | 4.17% | NA |
| Intermediate | 90 | 82.20% | 6.70% | 5.56% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0620619372 | C -> T | LOC_Os06g35360.1 | splice_donor_variant&intron_variant ; HIGH | splice_donor_variant | Average:9.116; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |
| vg0620619372 | C -> DEL | LOC_Os06g35360.1 | N | splice_donor_variant | Average:9.116; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0620619372 | 3.65E-06 | 3.65E-06 | mr1473_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 |
| vg0620619372 | 6.53E-06 | 6.53E-06 | mr1630_2 | Ind_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 |