Search for Variation information by Variation ID:
Detailed information for vg1120445376:
| Variant ID: vg1120445376 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 20445376 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CATGATCATGTGTCTTGTGCACATCGATGAATAATTTAAGTGTTCGAAGATTCTGCATGGCTCCTTGTGCAAACTCGATCTCCATGGTGTCACTCCAGTA[C/A]
TCGAAAAGTGATAGGCACTTGAATCGGTAGCTGATTATCAGCCTCTCATCCCTGTCCACTGTGGGTTTCTCCACTCCTAGATAGAGACGACTAAGAGATG
Reverse complement sequence
CATCTCTTAGTCGTCTCTATCTAGGAGTGGAGAAACCCACAGTGGACAGGGATGAGAGGCTGATAATCAGCTACCGATTCAAGTGCCTATCACTTTTCGA[G/T]
TACTGGAGTGACACCATGGAGATCGAGTTTGCACAAGGAGCCATGCAGAATCTTCGAACACTTAAATTATTCATCGATGTGCACAAGACACATGATCATG
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 75.00% | 3.50% | 1.14% | 20.38% | NA |
| All Indica | 2759 | 70.40% | 0.50% | 0.98% | 28.13% | NA |
| All Japonica | 1512 | 85.40% | 9.70% | 1.19% | 3.70% | NA |
| Aus | 269 | 55.80% | 0.00% | 2.97% | 41.26% | NA |
| Indica I | 595 | 52.80% | 0.20% | 1.01% | 46.05% | NA |
| Indica II | 465 | 78.50% | 0.60% | 1.51% | 19.35% | NA |
| Indica III | 913 | 71.90% | 0.00% | 0.99% | 27.16% | NA |
| Indica Intermediate | 786 | 77.20% | 1.30% | 0.64% | 20.87% | NA |
| Temperate Japonica | 767 | 79.30% | 17.50% | 1.96% | 1.30% | NA |
| Tropical Japonica | 504 | 90.90% | 0.00% | 0.40% | 8.73% | NA |
| Japonica Intermediate | 241 | 93.40% | 5.40% | 0.41% | 0.83% | NA |
| VI/Aromatic | 96 | 86.50% | 0.00% | 1.04% | 12.50% | NA |
| Intermediate | 90 | 87.80% | 3.30% | 0.00% | 8.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1120445376 | C -> A | LOC_Os11g34880.1 | missense_variant ; p.Glu504Asp; MODERATE | nonsynonymous_codon ; E504D | Average:42.013; most accessible tissue: Callus, score: 85.408 | benign  |
1.055 |
TOLERATED | 0.36 |
| vg1120445376 | C -> DEL | LOC_Os11g34880.1 | N | frameshift_variant | Average:42.013; most accessible tissue: Callus, score: 85.408 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1120445376 | NA | 2.09E-06 | mr1062 | 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 |
| vg1120445376 | NA | 3.55E-07 | mr1310 | 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 |
| vg1120445376 | 7.80E-06 | 7.80E-06 | mr1456 | 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 |
| vg1120445376 | NA | 3.59E-06 | mr1959 | 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 |