Search for Variation information by Variation ID:
Detailed information for vg1200182957:
| Variant ID: vg1200182957 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 182957 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CAGTTTCTTTGTCCTCGTTTCTTGTTGATTGCAGGATCAAATCAACTGGCACGATAGCATACCCGAAGGCGAGTTTTGGACCTGCACTGGAGTTAAGCAG[A/T]
TCTCCCAGGCCTCGTGTTTTTACGTCAACACGCTTTTGGCACGCCCGGTGGGACAGATCAGAAGTCAGAATCACAACAGCAATTTTCCTCATGGCCGAGA
Reverse complement sequence
TCTCGGCCATGAGGAAAATTGCTGTTGTGATTCTGACTTCTGATCTGTCCCACCGGGCGTGCCAAAAGCGTGTTGACGTAAAAACACGAGGCCTGGGAGA[T/A]
CTGCTTAACTCCAGTGCAGGTCCAAAACTCGCCTTCGGGTATGCTATCGTGCCAGTTGATTTGATCCTGCAATCAACAAGAAACGAGGACAAAGAAACTG
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 54.80% | 0.80% | 3.96% | 40.44% | NA |
| All Indica | 2759 | 30.40% | 0.00% | 5.51% | 64.08% | NA |
| All Japonica | 1512 | 92.40% | 2.40% | 1.85% | 3.37% | NA |
| Aus | 269 | 73.20% | 0.00% | 0.74% | 26.02% | NA |
| Indica I | 595 | 32.30% | 0.20% | 6.39% | 61.18% | NA |
| Indica II | 465 | 17.60% | 0.00% | 5.59% | 76.77% | NA |
| Indica III | 913 | 34.70% | 0.00% | 4.93% | 60.35% | NA |
| Indica Intermediate | 786 | 31.40% | 0.00% | 5.47% | 63.10% | NA |
| Temperate Japonica | 767 | 87.50% | 4.70% | 3.13% | 4.69% | NA |
| Tropical Japonica | 504 | 97.20% | 0.00% | 0.60% | 2.18% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.00% | 0.41% | 1.66% | NA |
| VI/Aromatic | 96 | 96.90% | 0.00% | 2.08% | 1.04% | NA |
| Intermediate | 90 | 73.30% | 0.00% | 3.33% | 23.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1200182957 | A -> DEL | LOC_Os12g01320.1 | N | frameshift_variant | Average:11.139; most accessible tissue: Callus, score: 27.862 | N | N | N | N |
| vg1200182957 | A -> T | LOC_Os12g01320.1 | missense_variant ; p.Arg431Ser; MODERATE | nonsynonymous_codon ; R431S | Average:11.139; most accessible tissue: Callus, score: 27.862 | benign  |
1.485 |
DELETERIOUS | 0.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1200182957 | NA | 9.67E-06 | mr1652 | 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 |
| vg1200182957 | NA | 6.06E-06 | mr1164_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 |
| vg1200182957 | NA | 3.68E-06 | mr1510_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 |
| vg1200182957 | NA | 4.57E-07 | mr1875_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 |
| vg1200182957 | 1.91E-06 | 1.91E-06 | mr1908_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 |