Search for Variation information by Variation ID:
Detailed information for vg0908524458:
| Variant ID: vg0908524458 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 8524458 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 119. )
Flanking Sequence (100 bp) in Reference Genome:
GAAGTGGAAGACGACAATATTCTGGACTTTGCTCAGTACGTTGGATTTGAAGGAAATCAAACGGGTGAGGAGGAAAGGGATGCTGATGGTAACGACGATG[C/T]
GGATGATCTTGGTCAGTTGTTGCAGGACGCCAAGGAGGACTGCGAAAGTGAAAAGGGGGCCCATAAATTGGACAAGATGTTAGAGGACCACAAAACGTCA
Reverse complement sequence
TGACGTTTTGTGGTCCTCTAACATCTTGTCCAATTTATGGGCCCCCTTTTCACTTTCGCAGTCCTCCTTGGCGTCCTGCAACAACTGACCAAGATCATCC[G/A]
CATCGTCGTTACCATCAGCATCCCTTTCCTCCTCACCCGTTTGATTTCCTTCAAATCCAACGTACTGAGCAAAGTCCAGAATATTGTCGTCTTCCACTTC
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 | 67.90% | 10.50% | 19.57% | 2.07% | NA |
| All Indica | 2759 | 46.90% | 17.40% | 32.44% | 3.33% | NA |
| All Japonica | 1512 | 99.80% | 0.00% | 0.20% | 0.00% | NA |
| Aus | 269 | 85.10% | 4.50% | 8.18% | 2.23% | NA |
| Indica I | 595 | 16.80% | 18.50% | 61.85% | 2.86% | NA |
| Indica II | 465 | 76.10% | 5.40% | 14.62% | 3.87% | NA |
| Indica III | 913 | 47.40% | 23.40% | 25.19% | 3.94% | NA |
| Indica Intermediate | 786 | 51.70% | 16.50% | 29.13% | 2.67% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.40% | 0.00% | 0.60% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 90.00% | 4.40% | 5.56% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0908524458 | C -> DEL | LOC_Os09g14430.1 | N | frameshift_variant | Average:23.805; most accessible tissue: Minghui63 flag leaf, score: 51.386 | N | N | N | N |
| vg0908524458 | C -> T | LOC_Os09g14430.1 | missense_variant ; p.Ala38Val; MODERATE | nonsynonymous_codon ; A38V | Average:23.805; most accessible tissue: Minghui63 flag leaf, score: 51.386 | benign  |
0.575 |
DELETERIOUS | 0.02 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0908524458 | NA | 1.74E-06 | mr1415_2 | 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 |
| vg0908524458 | NA | 3.98E-06 | mr1415_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 |
| vg0908524458 | NA | 2.63E-06 | mr1592_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 |
| vg0908524458 | NA | 1.49E-09 | mr1649_2 | 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 |
| vg0908524458 | 2.64E-06 | 2.64E-06 | mr1884_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 |