Search for Variation information by Variation ID:
Detailed information for vg1112981588:
| Variant ID: vg1112981588 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 12981588 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 94. )
Flanking Sequence (100 bp) in Reference Genome:
TATCGGTTTGGCTAGGAAGTCAACTTCCTCAATTCTAAGGTTAACTTCCGGGCATATTTGAGTTGCCCTTATATTCCTTCCAGGGGAATGTACTATCATT[G/A]
GTACATGTAAATTTTGGGTTTTCCAACCATTTCTTTTCACAAAAGCTTGTGATATGAAAGAATGGGAAGCTCCTGAATCAAACAGAACTATTGCGGGTAC
Reverse complement sequence
GTACCCGCAATAGTTCTGTTTGATTCAGGAGCTTCCCATTCTTTCATATCACAAGCTTTTGTGAAAAGAAATGGTTGGAAAACCCAAAATTTACATGTAC[C/T]
AATGATAGTACATTCCCCTGGAAGGAATATAAGGGCAACTCAAATATGCCCGGAAGTTAACCTTAGAATTGAGGAAGTTGACTTCCTAGCCAAACCGATA
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 | 64.20% | 2.00% | 25.67% | 8.17% | NA |
| All Indica | 2759 | 41.80% | 3.30% | 42.19% | 12.72% | NA |
| All Japonica | 1512 | 97.60% | 0.10% | 0.79% | 1.46% | NA |
| Aus | 269 | 90.30% | 0.40% | 8.18% | 1.12% | NA |
| Indica I | 595 | 64.50% | 1.30% | 26.72% | 7.39% | NA |
| Indica II | 465 | 39.10% | 1.30% | 46.45% | 13.12% | NA |
| Indica III | 913 | 26.60% | 5.30% | 50.49% | 17.63% | NA |
| Indica Intermediate | 786 | 43.80% | 3.70% | 41.73% | 10.81% | NA |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.13% | 0.13% | NA |
| Tropical Japonica | 504 | 93.80% | 0.40% | 1.59% | 4.17% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.00% | 1.24% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 2.08% | 0.00% | NA |
| Intermediate | 90 | 74.40% | 0.00% | 14.44% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1112981588 | G -> A | LOC_Os11g22570.1 | missense_variant ; p.Pro553Leu; MODERATE | nonsynonymous_codon ; P553L | Average:16.505; most accessible tissue: Zhenshan97 root, score: 23.888 | probably damaging  |
2.029 |
DELETERIOUS | 0.01 |
| vg1112981588 | G -> DEL | LOC_Os11g22570.1 | N | frameshift_variant | Average:16.505; most accessible tissue: Zhenshan97 root, score: 23.888 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1112981588 | 9.94E-07 | 2.95E-06 | mr1836_2 | 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 |