Search for Variation information by Variation ID:
Detailed information for vg1105297664:
| Variant ID: vg1105297664 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5297664 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ATGTTGCCTGTTGCAGTTGCAACACTACAAGATTGATCAAGTGAATTACCAGCAAGTATTTTCAGTACGTACTCCCTCCTGAGAGACTCTGGAAGAGCGA[T/G]
AAGCATACTCATTTGAGCCGGCACTTTTACAAAAGCAGCTGCAGCATTGACAACTTCAGTACCAGTCAATCCAAGCTTTTGACACTCAAGAATAGCTTCG
Reverse complement sequence
CGAAGCTATTCTTGAGTGTCAAAAGCTTGGATTGACTGGTACTGAAGTTGTCAATGCTGCAGCTGCTTTTGTAAAAGTGCCGGCTCAAATGAGTATGCTT[A/C]
TCGCTCTTCCAGAGTCTCTCAGGAGGGAGTACGTACTGAAAATACTTGCTGGTAATTCACTTGATCAATCTTGTAGTGTTGCAACTGCAACAGGCAACAT
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 40.10% | 3.70% | 0.91% | 55.23% | NA |
| All Indica | 2759 | 33.60% | 1.10% | 0.87% | 64.44% | NA |
| All Japonica | 1512 | 59.50% | 9.30% | 0.26% | 31.02% | NA |
| Aus | 269 | 6.70% | 0.00% | 5.20% | 88.10% | NA |
| Indica I | 595 | 22.20% | 2.20% | 0.84% | 74.79% | NA |
| Indica II | 465 | 13.30% | 0.90% | 2.37% | 83.44% | NA |
| Indica III | 913 | 46.50% | 0.20% | 0.33% | 52.90% | NA |
| Indica Intermediate | 786 | 39.10% | 1.50% | 0.64% | 58.78% | NA |
| Temperate Japonica | 767 | 60.80% | 17.20% | 0.13% | 21.90% | NA |
| Tropical Japonica | 504 | 67.90% | 0.40% | 0.40% | 31.35% | NA |
| Japonica Intermediate | 241 | 37.80% | 2.50% | 0.41% | 59.34% | NA |
| VI/Aromatic | 96 | 17.70% | 0.00% | 1.04% | 81.25% | NA |
| Intermediate | 90 | 41.10% | 5.60% | 0.00% | 53.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105297664 | T -> DEL | LOC_Os11g09900.1 | N | frameshift_variant | Average:8.267; most accessible tissue: Callus, score: 21.29 | N | N | N | N |
| vg1105297664 | T -> G | LOC_Os11g09900.1 | missense_variant ; p.Ile360Leu; MODERATE | nonsynonymous_codon ; I360L | Average:8.267; most accessible tissue: Callus, score: 21.29 | benign  |
-0.862 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1105297664 | 1.95E-06 | 1.36E-10 | mr1010_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 |
| vg1105297664 | NA | 8.84E-08 | mr1011_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 |
| vg1105297664 | NA | 1.40E-06 | mr1588_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 |
| vg1105297664 | NA | 6.10E-06 | mr1768_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 |