Search for Variation information by Variation ID:
Detailed information for vg0802282522:
| Variant ID: vg0802282522 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 2282522 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TGGCGTCTTGGAATGAACCATGATGAGCGGAATGCACATCGTTCCAGAATTTGCGATACTGGATAGCCTCCCAGTTGGATTCATCCTCGTCCTGCGACCG[C/T]
ATCGTCTCTAGGTATGCCTTGTCCTGCTCCTCGATGCTCTTCCTCACCCTCGCCTCCCACTCCTCCGCGGTTTCCATCCTCTTCCTGGGTCTCGACGCCT
Reverse complement sequence
AGGCGTCGAGACCCAGGAAGAGGATGGAAACCGCGGAGGAGTGGGAGGCGAGGGTGAGGAAGAGCATCGAGGAGCAGGACAAGGCATACCTAGAGACGAT[G/A]
CGGTCGCAGGACGAGGATGAATCCAACTGGGAGGCTATCCAGTATCGCAAATTCTGGAACGATGTGCATTCCGCTCATCATGGTTCATTCCAAGACGCCA
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 | 94.60% | 5.30% | 0.08% | 0.00% | NA |
| All Indica | 2759 | 95.90% | 4.00% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 51.30% | 47.60% | 1.12% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 93.10% | 6.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.70% | 1.30% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 91.30% | 8.50% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 94.80% | 5.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 7.80% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0802282522 | C -> T | LOC_Os08g04570.1 | missense_variant ; p.Met26Ile; MODERATE | nonsynonymous_codon ; M26I | Average:62.992; most accessible tissue: Callus, score: 86.893 | benign  |
-0.026 |
TOLERATED | 0.23 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0802282522 | NA | 2.63E-09 | mr1317_2 | 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 |
| vg0802282522 | NA | 2.37E-07 | mr1603_2 | 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 |
| vg0802282522 | NA | 1.03E-07 | mr1612_2 | 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 |
| vg0802282522 | NA | 6.03E-10 | mr1818_2 | 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 |
| vg0802282522 | 3.64E-06 | NA | mr1835_2 | 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 |