Search for Variation information by Variation ID:
Detailed information for vg0222029032:
| Variant ID: vg0222029032 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 22029032 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CAAGCCGGGAAGCAAGTTGGGAGTCCACATCCTATAAAAAACATCATGACTACAACAAGACCACTCGAGCTTCTTCATATGGATTTATTTGGGCCCGTGG[C/T]
CTACGTAAGCATTGGAGGTAATAAGTATGGTTTTGTTATTGTTGATGATTTTTCACGCTTCACTTGGGTGTACTTTCTCCATGACAAAAGCAAAGCTCAA
Reverse complement sequence
TTGAGCTTTGCTTTTGTCATGGAGAAAGTACACCCAAGTGAAGCGTGAAAAATCATCAACAATAACAAAACCATACTTATTACCTCCAATGCTTACGTAG[G/A]
CCACGGGCCCAAATAAATCCATATGAAGAAGCTCGAGTGGTCTTGTTGTAGTCATGATGTTTTTTATAGGATGTGGACTCCCAACTTGCTTCCCGGCTTG
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 63.20% | 36.60% | 0.13% | 0.00% | NA |
| All Indica | 2759 | 92.30% | 7.50% | 0.22% | 0.00% | NA |
| All Japonica | 1512 | 8.10% | 91.90% | 0.00% | 0.00% | NA |
| Aus | 269 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
| Indica I | 595 | 95.10% | 4.50% | 0.34% | 0.00% | NA |
| Indica II | 465 | 98.30% | 1.30% | 0.43% | 0.00% | NA |
| Indica III | 913 | 91.20% | 8.70% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 87.80% | 12.10% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 1.40% | 98.60% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 19.80% | 80.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 5.00% | 95.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 11.50% | 88.50% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 50.00% | 50.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0222029032 | C -> T | LOC_Os02g36470.1 | missense_variant ; p.Ala869Val; MODERATE | nonsynonymous_codon ; A869V | Average:8.967; most accessible tissue: Callus, score: 28.057 | benign  |
0.593 |
TOLERATED | 0.12 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0222029032 | 4.28E-06 | 1.01E-11 | Awn_length | Ind_All | YES | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg0222029032 | NA | 1.45E-39 | mr1124 | 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 |
| vg0222029032 | NA | 4.18E-10 | mr1595_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 |
| vg0222029032 | NA | 2.89E-08 | mr1600_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 |