Search for Variation information by Variation ID:
Detailed information for vg1005112746:
| Variant ID: vg1005112746 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 5112746 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 103. )
Flanking Sequence (100 bp) in Reference Genome:
ACATTGGTCAGCAAAGCCTTTCGACAAGGGTTTTTCTGGCCAACAGCCCTTAAAGATGCATGCGACATGGTCCAGCGATGTGAAGCCTGTCAATTCCACA[G/T]
CAAACACACAAAACTACCTACACAAGCGCTTCAAACAATCCCTCTGACTTGGCCGTTCTCGTGCTGGGGGCTAGACATACTTGGGCCATTCCCACGAGGA
Reverse complement sequence
TCCTCGTGGGAATGGCCCAAGTATGTCTAGCCCCCAGCACGAGAACGGCCAAGTCAGAGGGATTGTTTGAAGCGCTTGTGTAGGTAGTTTTGTGTGTTTG[C/A]
TGTGGAATTGACAGGCTTCACATCGCTGGACCATGTCGCATGCATCTTTAAGGGCTGTTGGCCAGAAAAACCCTTGTCGAAAGGCTTTGCTGACCAATGT
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 54.10% | 0.10% | 14.11% | 31.63% | NA |
| All Indica | 2759 | 42.30% | 0.30% | 19.83% | 37.62% | NA |
| All Japonica | 1512 | 77.00% | 0.00% | 1.06% | 21.96% | NA |
| Aus | 269 | 41.30% | 0.00% | 34.57% | 24.16% | NA |
| Indica I | 595 | 64.50% | 0.00% | 8.07% | 27.39% | NA |
| Indica II | 465 | 37.20% | 0.60% | 11.83% | 50.32% | NA |
| Indica III | 913 | 26.90% | 0.00% | 33.30% | 39.76% | NA |
| Indica Intermediate | 786 | 46.30% | 0.50% | 17.81% | 35.37% | NA |
| Temperate Japonica | 767 | 85.80% | 0.00% | 0.39% | 13.82% | NA |
| Tropical Japonica | 504 | 65.90% | 0.00% | 1.79% | 32.34% | NA |
| Japonica Intermediate | 241 | 72.20% | 0.00% | 1.66% | 26.14% | NA |
| VI/Aromatic | 96 | 61.50% | 0.00% | 6.25% | 32.29% | NA |
| Intermediate | 90 | 62.20% | 0.00% | 5.56% | 32.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1005112746 | G -> T | LOC_Os10g09480.1 | missense_variant ; p.Ser508Ile; MODERATE | nonsynonymous_codon ; S508I | Average:15.672; most accessible tissue: Callus, score: 40.926 | probably damaging  |
2.265 |
DELETERIOUS | 0.00 |
| vg1005112746 | G -> DEL | LOC_Os10g09480.1 | N | frameshift_variant | Average:15.672; most accessible tissue: Callus, score: 40.926 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1005112746 | NA | 6.80E-08 | mr1220 | 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 |
| vg1005112746 | NA | 2.18E-06 | 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 |
| vg1005112746 | 1.51E-06 | 1.51E-06 | mr1540 | 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 |
| vg1005112746 | 2.01E-06 | 6.37E-06 | mr1721 | 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 |
| vg1005112746 | 1.30E-06 | 1.89E-06 | mr1732 | 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 |
| vg1005112746 | NA | 1.48E-06 | mr1886 | 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 |