| Variant ID: vg0811940095 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 11940095 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.63, G: 0.37, others allele: 0.00, population size: 35. )
ATTTGATCAGGCCCTCAGATAGCTAATCAAGCTTGGCCTTCTCTTCATGAACAAGCTGCCGATTGGCTTGGATTGTGGCCTCGATATCTTTGCGCTCCCA[A/G]
CATTCAGCTAGTCTCAGCTTGGCTTTCTCCAGCTTGAATTGATGCTGCTCAAGATAGACGGCAGGAGTAAGGACATCGGCTAGTTCATCTGGGATCAGAG
CTCTGATCCCAGATGAACTAGCCGATGTCCTTACTCCTGCCGTCTATCTTGAGCAGCATCAATTCAAGCTGGAGAAAGCCAAGCTGAGACTAGCTGAATG[T/C]
TGGGAGCGCAAAGATATCGAGGCCACAATCCAAGCCAATCGGCAGCTTGTTCATGAAGAGAAGGCCAAGCTTGATTAGCTATCTGAGGGCCTGATCAAAT
| 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 | 30.20% | 8.90% | 3.17% | 57.68% | NA |
| All Indica | 2759 | 15.70% | 8.90% | 4.39% | 71.04% | NA |
| All Japonica | 1512 | 51.40% | 10.40% | 0.73% | 37.43% | NA |
| Aus | 269 | 69.90% | 0.70% | 3.72% | 25.65% | NA |
| Indica I | 595 | 11.90% | 2.50% | 4.03% | 81.51% | NA |
| Indica II | 465 | 9.90% | 4.90% | 4.30% | 80.86% | NA |
| Indica III | 913 | 21.70% | 15.30% | 4.82% | 58.16% | NA |
| Indica Intermediate | 786 | 14.90% | 8.70% | 4.20% | 72.26% | NA |
| Temperate Japonica | 767 | 85.30% | 0.40% | 0.39% | 13.95% | NA |
| Tropical Japonica | 504 | 9.70% | 27.20% | 0.99% | 62.10% | NA |
| Japonica Intermediate | 241 | 30.70% | 7.50% | 1.24% | 60.58% | NA |
| VI/Aromatic | 96 | 2.10% | 7.30% | 4.17% | 86.46% | NA |
| Intermediate | 90 | 32.20% | 10.00% | 4.44% | 53.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0811940095 | A -> G | LOC_Os08g19940.1 | synonymous_variant ; p.Cys321Cys; LOW | synonymous_codon | Average:8.356; most accessible tissue: Callus, score: 26.126 | N | N | N | N |
| vg0811940095 | A -> DEL | LOC_Os08g19940.1 | N | frameshift_variant | Average:8.356; most accessible tissue: Callus, score: 26.126 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0811940095 | NA | 8.14E-07 | mr1134 | 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 |
| vg0811940095 | NA | 3.56E-06 | mr1135 | 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 |
| vg0811940095 | NA | 5.64E-07 | mr1504 | 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 |
| vg0811940095 | NA | 9.92E-08 | mr1654_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 |
| vg0811940095 | NA | 2.13E-06 | mr1654_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 |