Search for Variation information by Variation ID:
Detailed information for vg0410490234:
| Variant ID: vg0410490234 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 10490234 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, C: 0.02, others allele: 0.00, population size: 119. )
Flanking Sequence (100 bp) in Reference Genome:
GTCGGGCCACAGGCCAGTCACCTTTTTTCCTTGTCTATGGGGCAGAAGCAATGTTGCCGAGTGAAGTTGAATTCGAGTCTTTGCGCTTTCGAAATTTCCA[T/C]
GAAGAACGCTACGAAGAGGACCGAGTGGATGACTTGCACCGATTGGAAGAAGTCCGCGAAGCGGCTTTGATTCAGTCGGCTCGATACTTACAAGGGCTGC
Reverse complement sequence
GCAGCCCTTGTAAGTATCGAGCCGACTGAATCAAAGCCGCTTCGCGGACTTCTTCCAATCGGTGCAAGTCATCCACTCGGTCCTCTTCGTAGCGTTCTTC[A/G]
TGGAAATTTCGAAAGCGCAAAGACTCGAATTCAACTTCACTCGGCAACATTGCTTCTGCCCCATAGACAAGGAAAAAAGGTGACTGGCCTGTGGCCCGAC
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 | 84.10% | 0.50% | 4.78% | 10.64% | NA |
| All Indica | 2759 | 86.80% | 0.60% | 5.87% | 6.74% | NA |
| All Japonica | 1512 | 77.00% | 0.00% | 3.31% | 19.71% | NA |
| Aus | 269 | 92.90% | 1.90% | 3.72% | 1.49% | NA |
| Indica I | 595 | 78.50% | 1.20% | 8.07% | 12.27% | NA |
| Indica II | 465 | 90.10% | 0.40% | 3.87% | 5.59% | NA |
| Indica III | 913 | 91.20% | 0.10% | 4.27% | 4.38% | NA |
| Indica Intermediate | 786 | 86.00% | 0.80% | 7.25% | 5.98% | NA |
| Temperate Japonica | 767 | 97.40% | 0.00% | 0.13% | 2.48% | NA |
| Tropical Japonica | 504 | 43.70% | 0.00% | 8.73% | 47.62% | NA |
| Japonica Intermediate | 241 | 81.70% | 0.00% | 2.07% | 16.18% | NA |
| VI/Aromatic | 96 | 90.60% | 1.00% | 0.00% | 8.33% | NA |
| Intermediate | 90 | 86.70% | 1.10% | 4.44% | 7.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0410490234 | T -> C | LOC_Os04g18850.1 | synonymous_variant ; p.His801His; LOW | synonymous_codon | Average:11.894; most accessible tissue: Minghui63 panicle, score: 25.313 | N | N | N | N |
| vg0410490234 | T -> C | LOC_Os04g18850.1 | synonymous_variant ; p.His801His; LOW | nonsynonymous_codon ; H801R | Average:11.894; most accessible tissue: Minghui63 panicle, score: 25.313 | benign  |
-0.433 |
TOLERATED | 0.56 |
| vg0410490234 | T -> DEL | LOC_Os04g18850.1 | N | frameshift_variant | Average:11.894; most accessible tissue: Minghui63 panicle, score: 25.313 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0410490234 | NA | 4.26E-07 | mr1245 | 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 |
| vg0410490234 | NA | 2.50E-09 | mr1514 | 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 |
| vg0410490234 | NA | 2.50E-07 | mr1681 | 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 |
| vg0410490234 | 3.54E-06 | 3.52E-06 | mr1954 | 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 |