Search for Variation information by Variation ID:
Detailed information for vg1127979337:
| Variant ID: vg1127979337 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 27979337 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CAGCTTGCCATGGCAGCTCTCTCACCCCCGTGTTCCTCACATCCAGAGTCCGCAGATGCTTCAGCTCCCCGATTTGCGATGGCAGCTCTCTCACTGACGT[G/A]
TTCCTCACATCCAGAGTTTGTAGATGCTTCAGCTCCCCGATTTGCGACGGCAGCTCGCTGATATTCCACATGTTACTCACGTCCAGAGTCCGCAGATGTT
Reverse complement sequence
AACATCTGCGGACTCTGGACGTGAGTAACATGTGGAATATCAGCGAGCTGCCGTCGCAAATCGGGGAGCTGAAGCATCTACAAACTCTGGATGTGAGGAA[C/T]
ACGTCAGTGAGAGAGCTGCCATCGCAAATCGGGGAGCTGAAGCATCTGCGGACTCTGGATGTGAGGAACACGGGGGTGAGAGAGCTGCCATGGCAAGCTG
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 | 60.50% | 7.00% | 9.25% | 23.17% | NA |
| All Indica | 2759 | 51.70% | 11.00% | 7.97% | 29.29% | NA |
| All Japonica | 1512 | 71.60% | 0.70% | 11.90% | 15.81% | NA |
| Aus | 269 | 84.40% | 1.10% | 6.69% | 7.81% | NA |
| Indica I | 595 | 39.70% | 31.80% | 11.43% | 17.14% | NA |
| Indica II | 465 | 31.20% | 0.90% | 11.83% | 56.13% | NA |
| Indica III | 913 | 68.00% | 5.90% | 3.29% | 22.78% | NA |
| Indica Intermediate | 786 | 54.10% | 7.30% | 8.52% | 30.15% | NA |
| Temperate Japonica | 767 | 72.40% | 0.50% | 16.82% | 10.30% | NA |
| Tropical Japonica | 504 | 69.20% | 1.40% | 5.36% | 24.01% | NA |
| Japonica Intermediate | 241 | 73.90% | 0.00% | 9.96% | 16.18% | NA |
| VI/Aromatic | 96 | 60.40% | 10.40% | 11.46% | 17.71% | NA |
| Intermediate | 90 | 74.40% | 5.60% | 8.89% | 11.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1127979337 | G -> A | LOC_Os11g46200.1 | synonymous_variant ; p.Asn803Asn; LOW | synonymous_codon | Average:53.051; most accessible tissue: Zhenshan97 flag leaf, score: 80.588 | N | N | N | N |
| vg1127979337 | G -> A | LOC_Os11g46200.1 | synonymous_variant ; p.Asn803Asn; LOW | nonsynonymous_codon | Average:53.051; most accessible tissue: Zhenshan97 flag leaf, score: 80.588 | benign  |
1.327 |
TOLERATED | 0.38 |
| vg1127979337 | G -> DEL | LOC_Os11g46200.1 | N | frameshift_variant | Average:53.051; most accessible tissue: Zhenshan97 flag leaf, score: 80.588 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1127979337 | 6.73E-07 | 5.81E-06 | mr1569 | 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 |