| Variant ID: vg0900280507 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 280507 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, G: 0.02, others allele: 0.00, population size: 108. )
CAGTCAGGGGCTCCTGACAAGCTTCGGTTTCAGCTTCAGCCGACTGGTGTCCAGTCGGGGGTTGATCACCCGAGTCTACATTGTCGGTTGTCGGCTGGTT[A/G]
TCACTCGGATGGCCTTCGACAGTCGGCCCGGTTTCTTTGGAAGAACTCGTCTCCATGTTAGCCGGATTAGAGTCCTTTCTAGATGGATCTAGGTCGGATG
CATCCGACCTAGATCCATCTAGAAAGGACTCTAATCCGGCTAACATGGAGACGAGTTCTTCCAAAGAAACCGGGCCGACTGTCGAAGGCCATCCGAGTGA[T/C]
AACCAGCCGACAACCGACAATGTAGACTCGGGTGATCAACCCCCGACTGGACACCAGTCGGCTGAAGCTGAAACCGAAGCTTGTCAGGAGCCCCTGACTG
| 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 | 45.70% | 35.30% | 4.57% | 14.47% | NA |
| All Indica | 2759 | 26.50% | 55.10% | 6.09% | 12.36% | NA |
| All Japonica | 1512 | 83.70% | 0.20% | 0.66% | 15.48% | NA |
| Aus | 269 | 3.70% | 48.00% | 12.64% | 35.69% | NA |
| Indica I | 595 | 14.80% | 55.80% | 8.24% | 21.18% | NA |
| Indica II | 465 | 39.60% | 47.70% | 5.38% | 7.31% | NA |
| Indica III | 913 | 24.10% | 66.30% | 4.82% | 4.82% | NA |
| Indica Intermediate | 786 | 30.30% | 45.90% | 6.36% | 17.43% | NA |
| Temperate Japonica | 767 | 70.00% | 0.10% | 1.30% | 28.55% | NA |
| Tropical Japonica | 504 | 99.40% | 0.00% | 0.00% | 0.60% | NA |
| Japonica Intermediate | 241 | 94.20% | 0.80% | 0.00% | 4.98% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 70.00% | 15.60% | 4.44% | 10.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0900280507 | A -> G | LOC_Os09g01350.1 | synonymous_variant ; p.Asp417Asp; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0900280507 | A -> DEL | LOC_Os09g01350.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0900280507 | 2.41E-06 | NA | mr1151 | 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 |
| vg0900280507 | 8.32E-07 | 8.32E-07 | mr1151 | 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 |