Search for Variation information by Variation ID:
Detailed information for vg0412455370:
| Variant ID: vg0412455370 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 12455370 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.86, C: 0.14, others allele: 0.00, population size: 78. )
Flanking Sequence (100 bp) in Reference Genome:
CTCTAGATGGCCGAGCACCCACCCAACCACCGCGGAGAAGGCATGGATGATTTTGTGGCAGAATTGGCTCGCATGACACTGGTGGTGGGCTACCCCAACG[T/C]
GCCAGAGTACTCGACTGTTCCACCGCTCAGTGGCGAGCTTCCTCACCGTGTTCGCCTGGAGGTCCATGGCTATGTGGGTACCTGCCTCGCTAACATTGTG
Reverse complement sequence
CACAATGTTAGCGAGGCAGGTACCCACATAGCCATGGACCTCCAGGCGAACACGGTGAGGAAGCTCGCCACTGAGCGGTGGAACAGTCGAGTACTCTGGC[A/G]
CGTTGGGGTAGCCCACCACCAGTGTCATGCGAGCCAATTCTGCCACAAAATCATCCATGCCTTCTCCGCGGTGGTTGGGTGGGTGCTCGGCCATCTAGAG
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 54.50% | 36.40% | 5.78% | 3.30% | NA |
| All Indica | 2759 | 85.90% | 4.60% | 8.12% | 1.41% | NA |
| All Japonica | 1512 | 0.90% | 96.80% | 2.12% | 0.20% | NA |
| Aus | 269 | 53.90% | 1.10% | 4.09% | 40.89% | NA |
| Indica I | 595 | 76.50% | 4.90% | 17.82% | 0.84% | NA |
| Indica II | 465 | 90.30% | 6.00% | 3.23% | 0.43% | NA |
| Indica III | 913 | 89.30% | 3.60% | 5.26% | 1.86% | NA |
| Indica Intermediate | 786 | 86.50% | 4.60% | 7.00% | 1.91% | NA |
| Temperate Japonica | 767 | 0.40% | 99.30% | 0.26% | 0.00% | NA |
| Tropical Japonica | 504 | 1.00% | 94.40% | 4.17% | 0.40% | NA |
| Japonica Intermediate | 241 | 2.10% | 93.80% | 3.73% | 0.41% | NA |
| VI/Aromatic | 96 | 8.30% | 86.50% | 4.17% | 1.04% | NA |
| Intermediate | 90 | 43.30% | 51.10% | 2.22% | 3.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0412455370 | T -> C | LOC_Os04g22000.1 | missense_variant ; p.Val32Ala; MODERATE | nonsynonymous_codon ; V32T | Average:47.559; most accessible tissue: Zhenshan97 flag leaf, score: 73.119 | benign  |
0 |
DELETERIOUS | 0.02 |
| vg0412455370 | T -> C | LOC_Os04g22000.1 | missense_variant ; p.Val32Ala; MODERATE | nonsynonymous_codon ; V32A | Average:47.559; most accessible tissue: Zhenshan97 flag leaf, score: 73.119 | benign |
-0.382 |
TOLERATED | 1.00 |
| vg0412455370 | T -> DEL | LOC_Os04g22000.1 | N | frameshift_variant | Average:47.559; most accessible tissue: Zhenshan97 flag leaf, score: 73.119 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0412455370 | NA | 8.35E-07 | mr1527 | 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 |
| vg0412455370 | 2.80E-06 | 1.81E-06 | mr1737 | 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 |
| vg0412455370 | NA | 7.40E-07 | mr1781 | 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 |