Search for Variation information by Variation ID:
Detailed information for vg1101412031:
| Variant ID: vg1101412031 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 1412031 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, A: 0.06, others allele: 0.00, population size: 236. )
Flanking Sequence (100 bp) in Reference Genome:
TATTTCATCTTTCTCCAGTTTGAAGCTATTGTGATGCAGGCTAGTAGAGTGCCTAACATATAAGTTTCCATGCTTTCTATGCCGTCTTGCTGAAAAGTAC[G/A]
AAAGAGGAGTCCAAGTTTCTTGCAATGGACTATCGTGGGCCATATTTTGGTTGACTGCAAAGATCAAATAGATTTTTCCGTGGAAGGAGACAAGACGGTG
Reverse complement sequence
CACCGTCTTGTCTCCTTCCACGGAAAAATCTATTTGATCTTTGCAGTCAACCAAAATATGGCCCACGATAGTCCATTGCAAGAAACTTGGACTCCTCTTT[C/T]
GTACTTTTCAGCAAGACGGCATAGAAAGCATGGAAACTTATATGTTAGGCACTCTACTAGCCTGCATCACAATAGCTTCAAACTGGAGAAAGATGAAATA
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 | 63.20% | 36.80% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 98.20% | 1.80% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 3.60% | 96.40% | 0.07% | 0.00% | NA |
| Aus | 269 | 63.20% | 36.80% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.50% | 0.30% | 0.17% | 0.00% | NA |
| Indica II | 465 | 97.40% | 2.60% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 96.40% | 3.60% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 2.90% | 97.00% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 4.40% | 95.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 4.10% | 95.90% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 7.30% | 92.70% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 50.00% | 50.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1101412031 | G -> A | LOC_Os11g03640.1 | missense_variant ; p.Ser424Leu; MODERATE | nonsynonymous_codon ; S424L | Average:46.674; most accessible tissue: Minghui63 root, score: 56.226 | possibly damaging  |
1.521 |
DELETERIOUS | 0.04 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1101412031 | NA | 2.90E-06 | mr1203 | 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 |
| vg1101412031 | 1.85E-06 | 1.41E-07 | mr1395 | 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 |
| vg1101412031 | NA | 4.85E-07 | mr1618 | 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 |