Search for Variation information by Variation ID:
Detailed information for vg1127979682:
| Variant ID: vg1127979682 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 27979682 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TCTGTATCTCCTGTGGGAGCTTAGTGATTCGCGTACCCTTGAGACCTAGGTACTTGAGCAGCCTGAGGCTCTCTAGCTGCTCACATATCTTCTTCAGGTG[G/A]
GAGTCCTCTATACCGATATTATCTTCAAGGTCCAACACTCGCAATCTTTTAAACATATCCAAGGGGACTCCTATCACGTCGCCAAGGATGACAAGGCTGC
Reverse complement sequence
GCAGCCTTGTCATCCTTGGCGACGTGATAGGAGTCCCCTTGGATATGTTTAAAAGATTGCGAGTGTTGGACCTTGAAGATAATATCGGTATAGAGGACTC[C/T]
CACCTGAAGAAGATATGTGAGCAGCTAGAGAGCCTCAGGCTGCTCAAGTACCTAGGTCTCAAGGGTACGCGAATCACTAAGCTCCCACAGGAGATACAGA
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 | 42.80% | 16.00% | 1.12% | 40.03% | NA |
| All Indica | 2759 | 42.80% | 20.40% | 0.83% | 35.92% | NA |
| All Japonica | 1512 | 41.30% | 10.40% | 1.72% | 46.63% | NA |
| Aus | 269 | 58.70% | 1.50% | 1.12% | 38.66% | NA |
| Indica I | 595 | 17.50% | 41.00% | 1.01% | 40.50% | NA |
| Indica II | 465 | 46.20% | 1.50% | 1.72% | 50.54% | NA |
| Indica III | 913 | 52.90% | 21.40% | 0.33% | 25.41% | NA |
| Indica Intermediate | 786 | 48.30% | 14.90% | 0.76% | 36.01% | NA |
| Temperate Japonica | 767 | 29.90% | 15.80% | 2.35% | 52.02% | NA |
| Tropical Japonica | 504 | 55.80% | 5.00% | 1.19% | 38.10% | NA |
| Japonica Intermediate | 241 | 47.30% | 4.60% | 0.83% | 47.30% | NA |
| VI/Aromatic | 96 | 12.50% | 25.00% | 0.00% | 62.50% | NA |
| Intermediate | 90 | 54.40% | 8.90% | 1.11% | 35.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1127979682 | G -> A | LOC_Os11g46200.1 | synonymous_variant ; p.Ser688Ser; LOW | synonymous_codon | Average:43.882; most accessible tissue: Callus, score: 81.053 | N | N | N | N |
| vg1127979682 | G -> A | LOC_Os11g46200.1 | synonymous_variant ; p.Ser688Ser; LOW | nonsynonymous_codon ; S688F | Average:43.882; most accessible tissue: Callus, score: 81.053 | possibly damaging  |
1.806 |
DELETERIOUS | 0.01 |
| vg1127979682 | G -> DEL | LOC_Os11g46200.1 | N | frameshift_variant | Average:43.882; most accessible tissue: Callus, score: 81.053 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1127979682 | NA | 6.28E-06 | mr1555 | 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 |
| vg1127979682 | NA | 3.35E-06 | mr1609 | 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 |