Search for Variation information by Variation ID:
Detailed information for vg0509797528:
| Variant ID: vg0509797528 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 9797528 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, A: 0.01, others allele: 0.00, population size: 97. )
Flanking Sequence (100 bp) in Reference Genome:
CCCTCATGATCGTGATGAAGAGAAGTGCCGGGTCAAAGTCACTTTGAACAGTAATCCTGAAGATATACCATCAGGGATGTTCGAGGCTGGAGGTGGAAGC[T/A]
ACATTCATGCTTGTCAGGAGGTGGCAAGGATCACCATAGGAGAGCTCCGCGAAAGCTACAACGATCGGTTGGCCGACACCGAGTATCGCTACCATCCTCG
Reverse complement sequence
CGAGGATGGTAGCGATACTCGGTGTCGGCCAACCGATCGTTGTAGCTTTCGCGGAGCTCTCCTATGGTGATCCTTGCCACCTCCTGACAAGCATGAATGT[A/T]
GCTTCCACCTCCAGCCTCGAACATCCCTGATGGTATATCTTCAGGATTACTGTTCAAAGTGACTTTGACCCGGCACTTCTCTTCATCACGATCATGAGGG
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 92.70% | 6.00% | 1.21% | 0.11% | NA |
| All Indica | 2759 | 88.30% | 9.70% | 1.81% | 0.18% | NA |
| All Japonica | 1512 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Aus | 269 | 97.80% | 0.00% | 2.23% | 0.00% | NA |
| Indica I | 595 | 86.20% | 11.60% | 2.18% | 0.00% | NA |
| Indica II | 465 | 82.40% | 16.30% | 1.29% | 0.00% | NA |
| Indica III | 913 | 94.10% | 4.80% | 0.88% | 0.22% | NA |
| Indica Intermediate | 786 | 86.80% | 9.90% | 2.93% | 0.38% | NA |
| Temperate Japonica | 767 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 6.70% | 1.11% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0509797528 | T -> DEL | LOC_Os05g17120.1 | N | frameshift_variant | Average:48.24; most accessible tissue: Zhenshan97 flag leaf, score: 72.387 | N | N | N | N |
| vg0509797528 | T -> A | LOC_Os05g17120.1 | missense_variant ; p.Tyr1966Asn; MODERATE | nonsynonymous_codon ; Y1966N | Average:48.24; most accessible tissue: Zhenshan97 flag leaf, score: 72.387 | probably damaging  |
2.429 |
DELETERIOUS | 0.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0509797528 | NA | 2.42E-06 | mr1170_2 | 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 |
| vg0509797528 | NA | 4.05E-06 | mr1258_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 |