Search for Variation information by Variation ID:
Detailed information for vg0906131677:
| Variant ID: vg0906131677 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 6131677 |
| Reference Allele: T | Alternative Allele: G,A |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.88, G: 0.11, A: 0.01, others allele: 0.00, population size: 84. )
Flanking Sequence (100 bp) in Reference Genome:
AAATCCAAGCAGCTTCCCTGACGGTACTCCGAAGATGCATTTTTCAGGGTTTAGTTTCATCCTGAAAGCGCGGATGCTCGCGAAAGTTTCTTCGAGATCC[T/G,A]
TAATCAAATCATCCTTCTGCTTGGTCTTGACGACTACATCATCAACATAAGCTTCAACATTGCGGCCGATTTGAGTTGAAAAGCACCTCTGAATCATGCG
Reverse complement sequence
CGCATGATTCAGAGGTGCTTTTCAACTCAAATCGGCCGCAATGTTGAAGCTTATGTTGATGATGTAGTCGTCAAGACCAAGCAGAAGGATGATTTGATTA[A/C,T]
GGATCTCGAAGAAACTTTCGCGAGCATCCGCGCTTTCAGGATGAAACTAAACCCTGAAAAATGCATCTTCGGAGTACCGTCAGGGAAGCTGCTTGGATTT
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 32.90% | 12.50% | 4.10% | 50.47% | A: 0.04% |
| All Indica | 2759 | 10.00% | 17.90% | 1.52% | 70.53% | A: 0.04% |
| All Japonica | 1512 | 80.60% | 0.10% | 0.26% | 18.98% | NA |
| Aus | 269 | 1.50% | 26.80% | 51.67% | 20.07% | NA |
| Indica I | 595 | 18.80% | 17.50% | 0.84% | 62.86% | NA |
| Indica II | 465 | 10.10% | 12.50% | 0.43% | 76.99% | NA |
| Indica III | 913 | 4.30% | 17.70% | 1.64% | 76.34% | NA |
| Indica Intermediate | 786 | 9.90% | 21.60% | 2.54% | 65.78% | A: 0.13% |
| Temperate Japonica | 767 | 90.50% | 0.00% | 0.39% | 9.13% | NA |
| Tropical Japonica | 504 | 78.20% | 0.00% | 0.00% | 21.83% | NA |
| Japonica Intermediate | 241 | 54.40% | 0.80% | 0.41% | 44.40% | NA |
| VI/Aromatic | 96 | 12.50% | 15.60% | 6.25% | 65.62% | NA |
| Intermediate | 90 | 47.80% | 8.90% | 3.33% | 38.89% | A: 1.11% |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0906131677 | T -> G | LOC_Os09g11040.1 | missense_variant ; p.Lys1102Thr; MODERATE | nonsynonymous_codon ; K1102T | Average:6.319; most accessible tissue: Zhenshan97 flower, score: 9.663 | benign  |
-1.447 |
TOLERATED | 0.63 |
| vg0906131677 | T -> DEL | LOC_Os09g11040.1 | N | frameshift_variant | Average:6.319; most accessible tissue: Zhenshan97 flower, score: 9.663 | N | N | N | N |
| vg0906131677 | T -> A | LOC_Os09g11040.1 | missense_variant ; p.Lys1102Met; MODERATE | nonsynonymous_codon ; K1102M | Average:6.319; most accessible tissue: Zhenshan97 flower, score: 9.663 | benign |
-0.555 |
TOLERATED | 0.09 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0906131677 | NA | 3.54E-11 | mr1222 | 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 |