Search for Variation information by Variation ID:
Detailed information for vg0504466784:
| Variant ID: vg0504466784 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 4466784 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TTGAAGCCATTGAGAATCATGTTGGCCTTCTTTAACTCATCATCTCCACGCCCAAACTTCTTGAACAACAAGTATGGCATCAAATTCACGGCGGCACCTC[C/T]
ATCCACTAGGACCCTAGAGACCGGCTTCCCATCAATATGACCTTTGAGATAAAGAGGCTTCATATGACGGTTTGACTCATCGGGCTTCTCAAAAACCGCA
Reverse complement sequence
TGCGGTTTTTGAGAAGCCCGATGAGTCAAACCGTCATATGAAGCCTCTTTATCTCAAAGGTCATATTGATGGGAAGCCGGTCTCTAGGGTCCTAGTGGAT[G/A]
GAGGTGCCGCCGTGAATTTGATGCCATACTTGTTGTTCAAGAAGTTTGGGCGTGGAGATGATGAGTTAAAGAAGGCCAACATGATTCTCAATGGCTTCAA
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 | 94.50% | 1.30% | 4.15% | 0.04% | NA |
| All Indica | 2759 | 90.90% | 2.20% | 6.89% | 0.04% | NA |
| All Japonica | 1512 | 99.70% | 0.00% | 0.20% | 0.07% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.37% | 0.00% | NA |
| Indica I | 595 | 85.90% | 1.80% | 12.10% | 0.17% | NA |
| Indica II | 465 | 85.80% | 4.70% | 9.46% | 0.00% | NA |
| Indica III | 913 | 95.40% | 0.80% | 3.83% | 0.00% | NA |
| Indica Intermediate | 786 | 92.40% | 2.70% | 4.96% | 0.00% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.26% | 0.13% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 1.10% | 2.22% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0504466784 | C -> T | LOC_Os05g08190.1 | missense_variant ; p.Gly64Arg; MODERATE | nonsynonymous_codon ; G64R | Average:17.228; most accessible tissue: Callus, score: 45.891 | benign  |
1.452 |
DELETERIOUS | 0.01 |
| vg0504466784 | C -> DEL | LOC_Os05g08190.1 | N | frameshift_variant | Average:17.228; most accessible tissue: Callus, score: 45.891 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0504466784 | 4.62E-06 | NA | mr1679_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 |