Search for Variation information by Variation ID:
Detailed information for vg0314639120:
| Variant ID: vg0314639120 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 14639120 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ACCTCCTCTCTCGCGAAACTGGCGACGGCGATGGGGGAAATCCCCTCCAAGCATGCGGCCAGGATTGCGGAGGAGACGTCAAACGGAATCTACACCGGGG[C/T]
GTGTCATGTCCTCACGTGTGTAAGTCTGTTGCGTCCTGAACTCAATCTGCGCGAGATCTTGGACCAGGGGGCGGCCAGCGACACGCGTAAGGAGGTGATG
Reverse complement sequence
CATCACCTCCTTACGCGTGTCGCTGGCCGCCCCCTGGTCCAAGATCTCGCGCAGATTGAGTTCAGGACGCAACAGACTTACACACGTGAGGACATGACAC[G/A]
CCCCGGTGTAGATTCCGTTTGACGTCTCCTCCGCAATCCTGGCCGCATGCTTGGAGGGGATTTCCCCCATCGCCGTCGCCAGTTTCGCGAGAGAGGAGGT
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 | 56.70% | 2.40% | 30.79% | 10.07% | NA |
| All Indica | 2759 | 36.80% | 3.30% | 42.84% | 17.04% | NA |
| All Japonica | 1512 | 98.80% | 0.10% | 1.12% | 0.00% | NA |
| Aus | 269 | 9.70% | 7.40% | 82.16% | 0.74% | NA |
| Indica I | 595 | 30.80% | 2.50% | 47.06% | 19.66% | NA |
| Indica II | 465 | 15.30% | 7.30% | 64.52% | 12.90% | NA |
| Indica III | 913 | 53.60% | 1.20% | 27.16% | 18.07% | NA |
| Indica Intermediate | 786 | 34.70% | 3.90% | 45.04% | 16.28% | NA |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.26% | 0.00% | NA |
| Tropical Japonica | 504 | 97.60% | 0.00% | 2.38% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.40% | 1.24% | 0.00% | NA |
| VI/Aromatic | 96 | 89.60% | 0.00% | 9.38% | 1.04% | NA |
| Intermediate | 90 | 64.40% | 3.30% | 28.89% | 3.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0314639120 | C -> T | LOC_Os03g25580.1 | missense_variant ; p.Ala449Val; MODERATE | nonsynonymous_codon ; A449V | Average:41.714; most accessible tissue: Minghui63 flag leaf, score: 75.341 | benign  |
0.593 |
TOLERATED | 0.10 |
| vg0314639120 | C -> DEL | LOC_Os03g25580.1 | N | frameshift_variant | Average:41.714; most accessible tissue: Minghui63 flag leaf, score: 75.341 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0314639120 | 1.15E-07 | NA | mr1542 | 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 |
| vg0314639120 | 5.68E-08 | 2.15E-15 | mr1542 | 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 |
| vg0314639120 | 6.03E-06 | NA | mr1542_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 |
| vg0314639120 | 5.23E-07 | 7.67E-17 | mr1542_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 |