Search for Variation information by Variation ID:
Detailed information for vg1128247542:
| Variant ID: vg1128247542 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 28247542 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.01, others allele: 0.00, population size: 236. )
Flanking Sequence (100 bp) in Reference Genome:
TCTGTTCAACAACACGCCTTTGCTAACTTATCTCAACGTTGGTAACAATAGCCTGTCAGGACTGATACCGGGTTGCATCGGTTCCTTGCCAATCCTCCAA[C/T]
ACCTTAACTTTCAGGCCAATAACTTAACTGGGGCGGTGCCACCAGCCATCTTCAACATGTCTAAATTAAGTACCATTTCTCTTATATCGAATGGTTTAAC
Reverse complement sequence
GTTAAACCATTCGATATAAGAGAAATGGTACTTAATTTAGACATGTTGAAGATGGCTGGTGGCACCGCCCCAGTTAAGTTATTGGCCTGAAAGTTAAGGT[G/A]
TTGGAGGATTGGCAAGGAACCGATGCAACCCGGTATCAGTCCTGACAGGCTATTGTTACCAACGTTGAGATAAGTTAGCAAAGGCGTGTTGTTGAACAGA
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 | 64.00% | 10.60% | 1.40% | 23.99% | NA |
| All Indica | 2759 | 79.30% | 3.20% | 1.01% | 16.56% | NA |
| All Japonica | 1512 | 37.10% | 25.60% | 1.92% | 35.38% | NA |
| Aus | 269 | 43.50% | 7.10% | 2.60% | 46.84% | NA |
| Indica I | 595 | 73.90% | 0.70% | 1.68% | 23.70% | NA |
| Indica II | 465 | 90.80% | 4.30% | 0.00% | 4.95% | NA |
| Indica III | 913 | 81.80% | 1.50% | 0.66% | 15.99% | NA |
| Indica Intermediate | 786 | 73.50% | 6.20% | 1.53% | 18.70% | NA |
| Temperate Japonica | 767 | 41.10% | 32.70% | 2.48% | 23.73% | NA |
| Tropical Japonica | 504 | 33.90% | 12.90% | 1.39% | 51.79% | NA |
| Japonica Intermediate | 241 | 31.10% | 29.50% | 1.24% | 38.17% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 72.20% | 10.00% | 2.22% | 15.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1128247542 | C -> T | LOC_Os11g47000.1 | missense_variant ; p.His178Tyr; MODERATE | nonsynonymous_codon ; H178Y | Average:60.41; most accessible tissue: Zhenshan97 flag leaf, score: 74.498 | benign  |
0.241 |
TOLERATED | 1.00 |
| vg1128247542 | C -> DEL | LOC_Os11g47000.1 | N | frameshift_variant | Average:60.41; most accessible tissue: Zhenshan97 flag leaf, score: 74.498 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1128247542 | NA | 8.72E-06 | mr1439_2 | Ind_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 |
| vg1128247542 | 1.71E-06 | 2.84E-07 | mr1893_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 |