Search for Variation information by Variation ID:
Detailed information for vg1121620243:
| Variant ID: vg1121620243 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 21620243 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TTCTGCGAGATACTTGGATAACTCGGGGTTAGAGCATTTATAATCTTTGTGCACCTGGTTCGCGACTAGCTCGGAGTCCCCTTTGACGATTAGTCGCTTG[A/G]
CCCCAAGTGCAGCTGCAGCTCTTATCCCAACGAGTAGTCCTTCGTATTCTGCTGTGTTATTGGTTGCCCTGAAGTTGAGGTGGATTGCGTGCTTGAATTG
Reverse complement sequence
CAATTCAAGCACGCAATCCACCTCAACTTCAGGGCAACCAATAACACAGCAGAATACGAAGGACTACTCGTTGGGATAAGAGCTGCAGCTGCACTTGGGG[T/C]
CAAGCGACTAATCGTCAAAGGGGACTCCGAGCTAGTCGCGAACCAGGTGCACAAAGATTATAAATGCTCTAACCCCGAGTTATCCAAGTATCTCGCAGAA
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 | 60.40% | 20.00% | 13.86% | 5.73% | NA |
| All Indica | 2759 | 58.20% | 22.90% | 16.67% | 2.25% | NA |
| All Japonica | 1512 | 64.40% | 16.40% | 5.56% | 13.62% | NA |
| Aus | 269 | 71.40% | 15.20% | 13.01% | 0.37% | NA |
| Indica I | 595 | 56.80% | 23.90% | 17.98% | 1.34% | NA |
| Indica II | 465 | 67.70% | 20.20% | 11.61% | 0.43% | NA |
| Indica III | 913 | 53.50% | 23.70% | 19.17% | 3.72% | NA |
| Indica Intermediate | 786 | 59.00% | 22.90% | 15.78% | 2.29% | NA |
| Temperate Japonica | 767 | 85.40% | 3.00% | 3.13% | 8.47% | NA |
| Tropical Japonica | 504 | 38.50% | 35.90% | 9.13% | 16.47% | NA |
| Japonica Intermediate | 241 | 51.90% | 18.30% | 5.81% | 24.07% | NA |
| VI/Aromatic | 96 | 31.20% | 4.20% | 64.58% | 0.00% | NA |
| Intermediate | 90 | 58.90% | 23.30% | 15.56% | 2.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1121620243 | A -> DEL | LOC_Os11g36640.1 | N | frameshift_variant | Average:15.351; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |
| vg1121620243 | A -> G | LOC_Os11g36640.1 | missense_variant ; p.Val1354Ala; MODERATE | nonsynonymous_codon ; V1354A | Average:15.351; most accessible tissue: Zhenshan97 panicle, score: 20.424 | benign  |
0.337 |
TOLERATED | 0.24 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1121620243 | NA | 9.22E-06 | mr1138 | 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 |
| vg1121620243 | NA | 1.62E-06 | mr1176 | 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 |
| vg1121620243 | 1.61E-06 | 1.61E-06 | mr1866 | 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 |