Search for Variation information by Variation ID:
Detailed information for vg0507097189:
| Variant ID: vg0507097189 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 7097189 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TCGTTGTCGGCGTCGGAGTCCGACGAAGCAGGGACCCTTCGCTTCCTAGGGGCAAGCTTCACTTGCCCGCGCATTCGCTTTCGCGAAGGCCCTGCATCGT[C/T]
GTCCGCTTTGTGGGGGTTTGCCCGAGGAGGCAACTCGCTGTTATAAACCCGGTTCGCCCGCCCAGACGCTTGTCGTTAGGGATGACAACAGAGCGGATAC
Reverse complement sequence
GTATCCGCTCTGTTGTCATCCCTAACGACAAGCGTCTGGGCGGGCGAACCGGGTTTATAACAGCGAGTTGCCTCCTCGGGCAAACCCCCACAAAGCGGAC[G/A]
ACGATGCAGGGCCTTCGCGAAAGCGAATGCGCGGGCAAGTGAAGCTTGCCCCTAGGAAGCGAAGGGTCCCTGCTTCGTCGGACTCCGACGCCGACAACGA
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 | 60.90% | 3.40% | 1.48% | 34.17% | NA |
| All Indica | 2759 | 59.10% | 5.90% | 1.96% | 33.09% | NA |
| All Japonica | 1512 | 63.10% | 0.00% | 0.40% | 36.51% | NA |
| Aus | 269 | 87.40% | 0.00% | 2.23% | 10.41% | NA |
| Indica I | 595 | 73.60% | 10.80% | 1.01% | 14.62% | NA |
| Indica II | 465 | 33.80% | 1.30% | 3.87% | 61.08% | NA |
| Indica III | 913 | 56.60% | 5.40% | 1.86% | 36.14% | NA |
| Indica Intermediate | 786 | 65.90% | 5.50% | 1.65% | 26.97% | NA |
| Temperate Japonica | 767 | 91.90% | 0.00% | 0.26% | 7.82% | NA |
| Tropical Japonica | 504 | 20.20% | 0.00% | 0.60% | 79.17% | NA |
| Japonica Intermediate | 241 | 61.00% | 0.00% | 0.41% | 38.59% | NA |
| VI/Aromatic | 96 | 9.40% | 0.00% | 2.08% | 88.54% | NA |
| Intermediate | 90 | 56.70% | 0.00% | 2.22% | 41.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0507097189 | C -> T | LOC_Os05g12350.1 | missense_variant ; p.Asp253Asn; MODERATE | nonsynonymous_codon ; D253N | Average:31.945; most accessible tissue: Minghui63 panicle, score: 42.799 | benign  |
0.754 |
TOLERATED | 0.08 |
| vg0507097189 | C -> DEL | LOC_Os05g12350.1 | N | frameshift_variant | Average:31.945; most accessible tissue: Minghui63 panicle, score: 42.799 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0507097189 | 8.80E-07 | 2.68E-07 | mr1496_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 |