Search for Variation information by Variation ID:
Detailed information for vg0223405623:
| Variant ID: vg0223405623 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 23405623 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TATAACAAGGTCGACATGGATGGTCTCGGGCCAGTCGTACAGCCTCGGGAGGAACACCTTGTTGTGCATCAACCTAAGCTTAGTCTTCCTCAACATCGTC[G/A]
TGTATGTCCCGGTGAACAACGCATGTCCTTCCAATGACCGCATCTTCTCCCACTCCATCGTCTCTTCATTGAGCTTGACGACATGGACAGGCGCACCACT
Reverse complement sequence
AGTGGTGCGCCTGTCCATGTCGTCAAGCTCAATGAAGAGACGATGGAGTGGGAGAAGATGCGGTCATTGGAAGGACATGCGTTGTTCACCGGGACATACA[C/T]
GACGATGTTGAGGAAGACTAAGCTTAGGTTGATGCACAACAAGGTGTTCCTCCCGAGGCTGTACGACTGGCCCGAGACCATCCATGTCGACCTTGTTATA
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 88.80% | 9.80% | 1.38% | 0.00% | NA |
| All Indica | 2759 | 86.80% | 12.70% | 0.51% | 0.00% | NA |
| All Japonica | 1512 | 90.10% | 6.70% | 3.24% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 96.10% | 3.20% | 0.67% | 0.00% | NA |
| Indica II | 465 | 97.00% | 2.80% | 0.22% | 0.00% | NA |
| Indica III | 913 | 72.20% | 27.60% | 0.22% | 0.00% | NA |
| Indica Intermediate | 786 | 90.70% | 8.40% | 0.89% | 0.00% | NA |
| Temperate Japonica | 767 | 89.70% | 6.80% | 3.52% | 0.00% | NA |
| Tropical Japonica | 504 | 92.10% | 5.20% | 2.78% | 0.00% | NA |
| Japonica Intermediate | 241 | 87.10% | 9.50% | 3.32% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 86.70% | 11.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0223405623 | G -> A | LOC_Os02g38720.1 | missense_variant ; p.Thr292Met; MODERATE | nonsynonymous_codon ; T292M | Average:52.998; most accessible tissue: Zhenshan97 young leaf, score: 66.32 | probably damaging  |
2.97 |
DELETERIOUS | 0.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0223405623 | 3.67E-06 | NA | mr1719 | 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 |