Search for Variation information by Variation ID:
Detailed information for vg0322901276:
| Variant ID: vg0322901276 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 22901276 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AGTGACAAGGCATTTGGCGATTTATTGAAACTCATCAAGAACATTCTTCCGGAGGGAAACAAATTGCCCGAGACAACGTACGAGGCTAAGAAGATAGTCT[G/A]
CCATCTAGGACTGGAAGTTCAGAAGATTCACGCATGTTCGAATGATTGTATCCTATATCGCGGTGAGGAGTACGAGAACCTAGAAGCATGCCCTCTTTGC
Reverse complement sequence
GCAAAGAGGGCATGCTTCTAGGTTCTCGTACTCCTCACCGCGATATAGGATACAATCATTCGAACATGCGTGAATCTTCTGAACTTCCAGTCCTAGATGG[C/T]
AGACTATCTTCTTAGCCTCGTACGTTGTCTCGGGCAATTTGTTTCCCTCCGGAAGAATGTTCTTGATGAGTTTCAATAAATCGCCAAATGCCTTGTCACT
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 64.40% | 35.20% | 0.36% | 0.00% | NA |
| All Indica | 2759 | 98.70% | 1.20% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 0.60% | 99.30% | 0.07% | 0.00% | NA |
| Aus | 269 | 97.40% | 2.60% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.00% | 0.70% | 0.34% | 0.00% | NA |
| Indica II | 465 | 98.70% | 1.30% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 97.50% | 2.50% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 0.30% | 99.70% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 1.20% | 98.80% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 0.40% | 99.20% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 10.40% | 77.10% | 12.50% | 0.00% | NA |
| Intermediate | 90 | 45.60% | 52.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0322901276 | G -> A | LOC_Os03g41180.1 | missense_variant ; p.Cys132Tyr; MODERATE | nonsynonymous_codon ; C132Y | Average:17.334; most accessible tissue: Minghui63 panicle, score: 25.313 | benign  |
0.57 |
DELETERIOUS | 0.03 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0322901276 | NA | 2.75E-07 | mr1750 | 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 |
| vg0322901276 | NA | 6.23E-24 | mr1386_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 |
| vg0322901276 | NA | 4.49E-06 | mr1896_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 |
| vg0322901276 | 2.60E-07 | 4.48E-10 | mr1987_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 |