Search for Variation information by Variation ID:
Detailed information for vg1006468934:
| Variant ID: vg1006468934 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 6468934 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CGGTCATCATCATAAGTAGTGATGAAGAAGAAGAATCTAAGCGCAACCATTCCAAGATTGAGTGGGTAGCAACCCAAGATGATGAAGACGAGCCTTCAAT[T/C]
GACCTCCGATGCTTGGAAGAACTAGAGTGACTTGTTAAGTCGTTGTCTTAGATTGTTGTGTTAGTTTGCTTGCTTAAAGTTTGCTTGTGTGTGTCTCGCA
Reverse complement sequence
TGCGAGACACACACAAGCAAACTTTAAGCAAGCAAACTAACACAACAATCTAAGACAACGACTTAACAAGTCACTCTAGTTCTTCCAAGCATCGGAGGTC[A/G]
ATTGAAGGCTCGTCTTCATCATCTTGGGTTGCTACCCACTCAATCTTGGAATGGTTGCGCTTAGATTCTTCTTCTTCATCACTACTTATGATGATGACCG
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 25.30% | 0.20% | 45.51% | 28.99% | NA |
| All Indica | 2759 | 5.00% | 0.30% | 64.77% | 30.01% | NA |
| All Japonica | 1512 | 62.50% | 0.10% | 5.03% | 32.41% | NA |
| Aus | 269 | 0.70% | 0.40% | 91.82% | 7.06% | NA |
| Indica I | 595 | 3.50% | 0.00% | 45.71% | 50.76% | NA |
| Indica II | 465 | 5.40% | 0.90% | 60.43% | 33.33% | NA |
| Indica III | 913 | 5.10% | 0.10% | 77.55% | 17.20% | NA |
| Indica Intermediate | 786 | 5.60% | 0.30% | 66.92% | 27.23% | NA |
| Temperate Japonica | 767 | 70.50% | 0.00% | 1.96% | 27.51% | NA |
| Tropical Japonica | 504 | 51.60% | 0.20% | 9.52% | 38.69% | NA |
| Japonica Intermediate | 241 | 59.80% | 0.00% | 5.39% | 34.85% | NA |
| VI/Aromatic | 96 | 67.70% | 0.00% | 14.58% | 17.71% | NA |
| Intermediate | 90 | 52.20% | 0.00% | 30.00% | 17.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1006468934 | T -> C | LOC_Os10g11696.1 | synonymous_variant ; p.Ile252Ile; LOW | synonymous_codon | Average:13.213; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |
| vg1006468934 | T -> C | LOC_Os10g11696.1 | synonymous_variant ; p.Ile252Ile; LOW | nonsynonymous_codon ; I252N | Average:13.213; most accessible tissue: Zhenshan97 panicle, score: 20.424 | probably damaging  |
2.175 |
DELETERIOUS | 0.00 |
| vg1006468934 | T -> DEL | LOC_Os10g11696.1 | N | frameshift_variant | Average:13.213; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1006468934 | NA | 3.81E-07 | mr1038 | 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 |
| vg1006468934 | NA | 1.58E-07 | mr1570 | 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 |
| vg1006468934 | 9.70E-06 | 4.25E-06 | mr1653 | 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 |
| vg1006468934 | NA | 9.06E-07 | mr1389_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 |