Search for Variation information by Variation ID:
Detailed information for vg1123808197:
| Variant ID: vg1123808197 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 23808197 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 218. )
Flanking Sequence (100 bp) in Reference Genome:
CACTCTGGCCGGAGTTATGGCCACCCAAACTCAACTTCTGCAAGCTATCGCGAACAACTAAGGCAACCGCGGAGGGTCAAGCTTTGGAGAGTTCATGAGG[A/G]
CCAAGCCACCCACATTCGCCACAGCTGAAGAACCTATGGATGCTGAAGATTGTTTGAGGGTCATTGAGAAAAAGCTAACTCTTGTTCGAGTACGTGAGGC
Reverse complement sequence
GCCTCACGTACTCGAACAAGAGTTAGCTTTTTCTCAATGACCCTCAAACAATCTTCAGCATCCATAGGTTCTTCAGCTGTGGCGAATGTGGGTGGCTTGG[T/C]
CCTCATGAACTCTCCAAAGCTTGACCCTCCGCGGTTGCCTTAGTTGTTCGCGATAGCTTGCAGAAGTTGAGTTTGGGTGGCCATAACTCCGGCCAGAGTG
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 91.90% | 0.60% | 1.29% | 6.28% | NA |
| All Indica | 2759 | 97.60% | 0.10% | 0.76% | 1.59% | NA |
| All Japonica | 1512 | 79.20% | 1.60% | 2.58% | 16.67% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.37% | 0.00% | NA |
| Indica I | 595 | 98.50% | 0.00% | 0.84% | 0.67% | NA |
| Indica II | 465 | 93.10% | 0.00% | 1.51% | 5.38% | NA |
| Indica III | 913 | 99.00% | 0.00% | 0.66% | 0.33% | NA |
| Indica Intermediate | 786 | 97.80% | 0.30% | 0.38% | 1.53% | NA |
| Temperate Japonica | 767 | 66.10% | 2.20% | 3.65% | 28.03% | NA |
| Tropical Japonica | 504 | 96.60% | 0.20% | 0.60% | 2.58% | NA |
| Japonica Intermediate | 241 | 84.20% | 2.50% | 3.32% | 9.96% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 0.00% | 1.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1123808197 | A -> DEL | LOC_Os11g39950.1 | N | frameshift_variant | Average:35.069; most accessible tissue: Minghui63 panicle, score: 53.77 | N | N | N | N |
| vg1123808197 | A -> G | LOC_Os11g39950.1 | missense_variant ; p.Thr395Ala; MODERATE | nonsynonymous_codon ; T395A | Average:35.069; most accessible tissue: Minghui63 panicle, score: 53.77 | benign  |
0.781 |
TOLERATED | 0.09 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1123808197 | 2.67E-06 | 1.92E-06 | mr1129_2 | Jap_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 |
| vg1123808197 | NA | 6.09E-07 | mr1457_2 | Jap_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 |
| vg1123808197 | NA | 2.65E-07 | mr1458_2 | Jap_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 |