Search for Variation information by Variation ID:
Detailed information for vg0416101905:
| Variant ID: vg0416101905 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 16101905 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GATTGGAACTAATGTATTCTTGAAAAGCTGGAAAAATCGAAATAAGAATGTGGTTGTTGCTTCAATTGTAAGCTGTGATCCAACACGCAAAGTTGCAGGT[A/G]
TTGAGCTAGGAACTGAATACTTGATGGTGCATGTTCATTTTCCATTGGCAAAATATGAAGAATTGATCAGGCCATACAAAGGCTACAAAATTATTGGCAA
Reverse complement sequence
TTGCCAATAATTTTGTAGCCTTTGTATGGCCTGATCAATTCTTCATATTTTGCCAATGGAAAATGAACATGCACCATCAAGTATTCAGTTCCTAGCTCAA[T/C]
ACCTGCAACTTTGCGTGTTGGATCACAGCTTACAATTGAAGCAACAACCACATTCTTATTTCGATTTTTCCAGCTTTTCAAGAATACATTAGTTCCAATC
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 | 79.90% | 2.60% | 9.99% | 7.58% | NA |
| All Indica | 2759 | 77.10% | 2.70% | 11.56% | 8.70% | NA |
| All Japonica | 1512 | 99.20% | 0.10% | 0.53% | 0.20% | NA |
| Aus | 269 | 16.00% | 14.10% | 34.94% | 34.94% | NA |
| Indica I | 595 | 92.90% | 0.20% | 1.51% | 5.38% | NA |
| Indica II | 465 | 81.90% | 0.90% | 6.24% | 10.97% | NA |
| Indica III | 913 | 60.50% | 6.00% | 21.47% | 12.05% | NA |
| Indica Intermediate | 786 | 81.40% | 1.80% | 10.81% | 5.98% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 98.00% | 0.20% | 1.19% | 0.60% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 30.20% | 7.30% | 44.79% | 17.71% | NA |
| Intermediate | 90 | 84.40% | 2.20% | 8.89% | 4.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0416101905 | A -> DEL | LOC_Os04g27250.2 | N | frameshift_variant | Average:29.145; most accessible tissue: Minghui63 flower, score: 37.761 | N | N | N | N |
| vg0416101905 | A -> DEL | LOC_Os04g27250.1 | N | frameshift_variant | Average:29.145; most accessible tissue: Minghui63 flower, score: 37.761 | N | N | N | N |
| vg0416101905 | A -> DEL | LOC_Os04g27250.3 | N | frameshift_variant | Average:29.145; most accessible tissue: Minghui63 flower, score: 37.761 | N | N | N | N |
| vg0416101905 | A -> G | LOC_Os04g27250.1 | missense_variant ; p.Ile90Val; MODERATE | nonsynonymous_codon ; I90V | Average:29.145; most accessible tissue: Minghui63 flower, score: 37.761 | benign  |
-1.204 |
TOLERATED | 1.00 |
| vg0416101905 | A -> G | LOC_Os04g27250.2 | missense_variant ; p.Ile90Val; MODERATE | nonsynonymous_codon ; I90V | Average:29.145; most accessible tissue: Minghui63 flower, score: 37.761 | benign |
-1.204 |
TOLERATED | 1.00 |
| vg0416101905 | A -> G | LOC_Os04g27250.3 | missense_variant ; p.Ile68Val; MODERATE | nonsynonymous_codon ; I68V | Average:29.145; most accessible tissue: Minghui63 flower, score: 37.761 | benign |
-1.041 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0416101905 | 4.92E-06 | 1.39E-06 | mr1043_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 |
| vg0416101905 | 2.90E-06 | 2.90E-06 | mr1912_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 |