| Variant ID: vg0412949354 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 12949354 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CCTCTCGTCTAATCTTGTATCGTAGTGCTTTGCAAACAGGGCATGCTTCTAGGTTCTCGGACTCCTCACCACGATATAGGATACAATCATTCGGACATGC[A/G]
TGAATCTTCTGAACTTCCAGTCCTAGAGGGCAGACTATCTTCTTAGCCTCGTACGTTGTCTTGGACAATTTGTTTCCCTCCAGAAGAATGTTCTTGACGA
TCGTCAAGAACATTCTTCTGGAGGGAAACAAATTGTCCAAGACAACGTACGAGGCTAAGAAGATAGTCTGCCCTCTAGGACTGGAAGTTCAGAAGATTCA[T/C]
GCATGTCCGAATGATTGTATCCTATATCGTGGTGAGGAGTCCGAGAACCTAGAAGCATGCCCTGTTTGCAAAGCACTACGATACAAGATTAGACGAGAGG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 54.90% | 4.30% | 6.05% | 34.74% | NA |
| All Indica | 2759 | 31.50% | 5.00% | 8.81% | 54.69% | NA |
| All Japonica | 1512 | 94.20% | 3.30% | 1.19% | 1.32% | NA |
| Aus | 269 | 56.90% | 4.80% | 7.06% | 31.23% | NA |
| Indica I | 595 | 17.10% | 4.00% | 7.23% | 71.60% | NA |
| Indica II | 465 | 32.00% | 6.20% | 11.61% | 50.11% | NA |
| Indica III | 913 | 42.80% | 4.70% | 7.78% | 44.69% | NA |
| Indica Intermediate | 786 | 28.90% | 5.30% | 9.54% | 56.23% | NA |
| Temperate Japonica | 767 | 95.20% | 1.80% | 1.43% | 1.56% | NA |
| Tropical Japonica | 504 | 99.40% | 0.00% | 0.20% | 0.40% | NA |
| Japonica Intermediate | 241 | 80.10% | 14.90% | 2.49% | 2.49% | NA |
| VI/Aromatic | 96 | 90.60% | 0.00% | 0.00% | 9.38% | NA |
| Intermediate | 90 | 67.80% | 3.30% | 6.67% | 22.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0412949354 | A -> DEL | LOC_Os04g22850.1 | N | frameshift_variant | Average:7.407; most accessible tissue: Callus, score: 13.318 | N | N | N | N |
| vg0412949354 | A -> G | LOC_Os04g22850.1 | synonymous_variant ; p.His142His; LOW | synonymous_codon | Average:7.407; most accessible tissue: Callus, score: 13.318 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0412949354 | 9.86E-06 | 9.86E-06 | mr1287 | 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 |
| vg0412949354 | 1.24E-06 | 1.24E-06 | mr1303 | 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 |