Search for Variation information by Variation ID:
Detailed information for vg1125482367:
| Variant ID: vg1125482367 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 25482367 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ATTTCAAGACCACCGCAAGGAGCTCAACCATATCTTCGGCGGCCCCCTGGCTTATGAGTCTAAAAGGAAGCAAAAGTTGACTGAACGGGAGATCAATGCT[G/A]
TCCAGCCCGACACGCCTCAGTATCTTCGATGGTCAGAGATTGCAATCAAGTTTGACCGCTCGGATCATCCCGACCGAGTGGTCCACCCGGGGCGGTACCC
Reverse complement sequence
GGGTACCGCCCCGGGTGGACCACTCGGTCGGGATGATCCGAGCGGTCAAACTTGATTGCAATCTCTGACCATCGAAGATACTGAGGCGTGTCGGGCTGGA[C/T]
AGCATTGATCTCCCGTTCAGTCAACTTTTGCTTCCTTTTAGACTCATAAGCCAGGGGGCCGCCGAAGATATGGTTGAGCTCCTTGCGGTGGTCTTGAAAT
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.00% | 1.50% | 0.51% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.00% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 94.20% | 4.40% | 1.39% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.60% | 0.10% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 99.30% | 0.50% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 86.90% | 10.50% | 2.58% | 0.00% | NA |
| Japonica Intermediate | 241 | 93.40% | 3.70% | 2.90% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 4.40% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1125482367 | G -> A | LOC_Os11g42320.1 | missense_variant ; p.Val744Ile; MODERATE | nonsynonymous_codon ; V744I | Average:53.559; most accessible tissue: Zhenshan97 flag leaf, score: 85.638 | benign  |
0.289 |
TOLERATED | 0.06 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1125482367 | 2.99E-06 | NA | mr1150_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 |