Search for Variation information by Variation ID:
Detailed information for vg0117137382:
| Variant ID: vg0117137382 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 17137382 |
| Reference Allele: T | Alternative Allele: C,G,A |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.50, T: 0.50, others allele: 0.00, population size: 104. )
Flanking Sequence (100 bp) in Reference Genome:
GAGCATTGGCATCCACATTAGGCTTGCCACAGAACGGGCTAGCCTGCGCCATTGTGATAAGGCTGGACTTCAAGTCGAAATCCATGTCTCCTATGTTGAT[T/C,G,A]
TGCGGCCCAATGGCCACATTGTCAGTAGAGGGAGCAGCGAACTCGCGAAGAGTCTTGCTGGCCATAGTATTGAAGATCGGTGGCGCTGGTATGGCTGGTT
Reverse complement sequence
AACCAGCCATACCAGCGCCACCGATCTTCAATACTATGGCCAGCAAGACTCTTCGCGAGTTCGCTGCTCCCTCTACTGACAATGTGGCCATTGGGCCGCA[A/G,C,T]
ATCAACATAGGAGACATGGATTTCGACTTGAAGTCCAGCCTTATCACAATGGCGCAGGCTAGCCCGTTCTGTGGCAAGCCTAATGTGGATGCCAATGCTC
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 | 41.50% | 38.40% | 4.51% | 15.43% | G: 0.17%; A: 0.02% |
| All Indica | 2759 | 66.10% | 4.20% | 6.71% | 22.98% | G: 0.04% |
| All Japonica | 1512 | 2.50% | 97.40% | 0.07% | 0.00% | NA |
| Aus | 269 | 27.90% | 32.30% | 7.06% | 30.11% | G: 2.60% |
| Indica I | 595 | 91.40% | 1.80% | 0.67% | 6.05% | NA |
| Indica II | 465 | 42.60% | 6.50% | 15.05% | 35.91% | NA |
| Indica III | 913 | 59.70% | 2.70% | 7.56% | 29.90% | G: 0.11% |
| Indica Intermediate | 786 | 68.30% | 6.20% | 5.34% | 20.10% | NA |
| Temperate Japonica | 767 | 0.90% | 99.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 5.40% | 94.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 1.70% | 97.90% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 0.00% | 93.80% | 1.04% | 5.21% | NA |
| Intermediate | 90 | 24.40% | 56.70% | 7.78% | 10.00% | A: 1.11% |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0117137382 | T -> G | LOC_Os01g31320.1 | missense_variant ; p.Gln22His; MODERATE | nonsynonymous_codon ; Q22H | Average:32.466; most accessible tissue: Zhenshan97 flag leaf, score: 70.837 | benign  |
0.341 |
TOLERATED | 0.05 |
| vg0117137382 | T -> A | LOC_Os01g31320.1 | missense_variant ; p.Gln22His; MODERATE | nonsynonymous_codon ; Q22H | Average:32.466; most accessible tissue: Zhenshan97 flag leaf, score: 70.837 | benign |
0.341 |
TOLERATED | 0.05 |
| vg0117137382 | T -> DEL | LOC_Os01g31320.1 | N | frameshift_variant | Average:32.466; most accessible tissue: Zhenshan97 flag leaf, score: 70.837 | N | N | N | N |
| vg0117137382 | T -> C | LOC_Os01g31320.1 | synonymous_variant ; p.Gln22Gln; LOW | synonymous_codon | Average:32.466; most accessible tissue: Zhenshan97 flag leaf, score: 70.837 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0117137382 | NA | 1.34E-06 | mr1503 | 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 |