Search for Variation information by Variation ID:
Detailed information for vg0909710935:
| Variant ID: vg0909710935 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 9710935 |
| Reference Allele: C | Alternative Allele: A,T |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GCGACAAAGCCACCTGTCCCGGAGATGGTGCACACTCCACTGATCCCTACACCTTCTCCGCAGCTGGGTTCCAGTTTGGAGACTCCGATCCAGGTTGACT[C/A,T]
CGAGACAGAGGGGACCGACACCGAGCCAGAGATCGAGCCAGACATCACTGATCCTTCAGAGGCTGAGACCCCTGTTCCCCGCATCACCTTCCTCGGAGGC
Reverse complement sequence
GCCTCCGAGGAAGGTGATGCGGGGAACAGGGGTCTCAGCCTCTGAAGGATCAGTGATGTCTGGCTCGATCTCTGGCTCGGTGTCGGTCCCCTCTGTCTCG[G/T,A]
AGTCAACCTGGATCGGAGTCTCCAAACTGGAACCCAGCTGCGGAGAAGGTGTAGGGATCAGTGGAGTGTGCACCATCTCCGGGACAGGTGGCTTTGTCGC
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 59.30% | 7.30% | 8.78% | 24.61% | NA |
| All Indica | 2759 | 47.80% | 9.70% | 12.87% | 29.58% | NA |
| All Japonica | 1512 | 77.60% | 3.00% | 2.38% | 17.00% | NA |
| Aus | 269 | 75.50% | 0.00% | 5.20% | 19.33% | NA |
| Indica I | 595 | 19.50% | 22.70% | 22.02% | 35.80% | NA |
| Indica II | 465 | 44.70% | 4.50% | 15.70% | 35.05% | NA |
| Indica III | 913 | 68.80% | 4.10% | 5.04% | 22.12% | NA |
| Indica Intermediate | 786 | 46.80% | 9.50% | 13.36% | 30.28% | NA |
| Temperate Japonica | 767 | 82.90% | 0.00% | 1.56% | 15.51% | NA |
| Tropical Japonica | 504 | 70.20% | 7.90% | 2.58% | 19.25% | NA |
| Japonica Intermediate | 241 | 76.30% | 2.10% | 4.56% | 17.01% | NA |
| VI/Aromatic | 96 | 45.80% | 30.20% | 7.29% | 16.67% | NA |
| Intermediate | 90 | 66.70% | 5.60% | 3.33% | 24.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0909710935 | C -> DEL | LOC_Os09g15890.1 | N | frameshift_variant | Average:9.403; most accessible tissue: Callus, score: 17.993 | N | N | N | N |
| vg0909710935 | C -> T | LOC_Os09g15890.1 | missense_variant ; p.Ser244Phe; MODERATE | N | Average:9.403; most accessible tissue: Callus, score: 17.993 | N | N | N | N |
| vg0909710935 | C -> T | LOC_Os09g15880.1 | upstream_gene_variant ; 3990.0bp to feature; MODIFIER | N | Average:9.403; most accessible tissue: Callus, score: 17.993 | N | N | N | N |
| vg0909710935 | C -> T | LOC_Os09g15900.1 | upstream_gene_variant ; 2664.0bp to feature; MODIFIER | N | Average:9.403; most accessible tissue: Callus, score: 17.993 | N | N | N | N |
| vg0909710935 | C -> A | LOC_Os09g15890.1 | missense_variant ; p.Ser244Tyr; MODERATE | nonsynonymous_codon ; S244Y | Average:9.403; most accessible tissue: Callus, score: 17.993 | possibly damaging  |
1.902 |
DELETERIOUS | 0.01 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0909710935 | 1.47E-06 | 1.47E-06 | mr1329_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 |
| vg0909710935 | 3.41E-06 | 3.41E-06 | mr1337_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 |