Search for Variation information by Variation ID:
Detailed information for vg1128368057:
| Variant ID: vg1128368057 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 28368057 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TTGTTTTTAATCAGGCAATTCAGGTACAATTTTAGCCGGAAGGATTTGGGTCGCTCAGGCAACAAGATATTTGCAAACCGGGACGGCGAGATGGTCGTCC[C/T]
TACGGAGCTTGACTGGGCCATCAGGGGAACAAATAGGTCATGCTCTGTCTGCGTCAGCGACCAAAGCGACTGCGCCAATGCCACTAACGGAGACGGGTAT
Reverse complement sequence
ATACCCGTCTCCGTTAGTGGCATTGGCGCAGTCGCTTTGGTCGCTGACGCAGACAGAGCATGACCTATTTGTTCCCCTGATGGCCCAGTCAAGCTCCGTA[G/A]
GGACGACCATCTCGCCGTCCCGGTTTGCAAATATCTTGTTGCCTGAGCGACCCAAATCCTTCCGGCTAAAATTGTACCTGAATTGCCTGATTAAAAACAA
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 59.50% | 11.50% | 1.21% | 27.87% | NA |
| All Indica | 2759 | 56.40% | 5.20% | 0.80% | 37.62% | NA |
| All Japonica | 1512 | 59.90% | 25.50% | 1.79% | 12.90% | NA |
| Aus | 269 | 77.30% | 2.20% | 2.60% | 17.84% | NA |
| Indica I | 595 | 45.90% | 1.30% | 0.67% | 52.10% | NA |
| Indica II | 465 | 74.80% | 4.30% | 0.86% | 20.00% | NA |
| Indica III | 913 | 43.00% | 8.10% | 0.66% | 48.19% | NA |
| Indica Intermediate | 786 | 69.00% | 5.20% | 1.02% | 24.81% | NA |
| Temperate Japonica | 767 | 53.80% | 33.40% | 2.35% | 10.43% | NA |
| Tropical Japonica | 504 | 67.30% | 12.70% | 1.19% | 18.85% | NA |
| Japonica Intermediate | 241 | 63.50% | 27.00% | 1.24% | 8.30% | NA |
| VI/Aromatic | 96 | 87.50% | 0.00% | 0.00% | 12.50% | NA |
| Intermediate | 90 | 63.30% | 8.90% | 1.11% | 26.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1128368057 | C -> T | LOC_Os11g47150.1 | missense_variant ; p.Pro263Leu; MODERATE | nonsynonymous_codon ; P263L | Average:14.659; most accessible tissue: Callus, score: 88.592 | probably damaging  |
2.029 |
DELETERIOUS | 0.00 |
| vg1128368057 | C -> DEL | LOC_Os11g47150.1 | N | frameshift_variant | Average:14.659; most accessible tissue: Callus, score: 88.592 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1128368057 | 6.02E-08 | 6.02E-08 | mr1828_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 |