Search for Variation information by Variation ID:
Detailed information for vg1006628058:
| Variant ID: vg1006628058 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 6628058 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GACGCTCGAGCACCTACTTCGCATCATTGACGGGTTCGCAAGGGGCGAGGAGAATTCCAAGCGACAGCAAGCTATACAAGCTGAGTATGACAAAGCCTCC[A/G]
TCGCCGCTGCTCAAGCTCAAGCACAAGTTCAAGTTGTCGAACCACCTCCCCTCTTCGTTCGCCAGTCTCAGCCGGCGATCCAAGGACAGCCGCCAAGGCA
Reverse complement sequence
TGCCTTGGCGGCTGTCCTTGGATCGCCGGCTGAGACTGGCGAACGAAGAGGGGAGGTGGTTCGACAACTTGAACTTGTGCTTGAGCTTGAGCAGCGGCGA[T/C]
GGAGGCTTTGTCATACTCAGCTTGTATAGCTTGCTGTCGCTTGGAATTCTCCTCGCCCCTTGCGAACCCGTCAATGATGCGAAGTAGGTGCTCGAGCGTC
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 | 19.10% | 2.50% | 2.88% | 75.56% | NA |
| All Indica | 2759 | 4.30% | 0.00% | 4.35% | 91.26% | NA |
| All Japonica | 1512 | 49.30% | 7.70% | 0.46% | 42.53% | NA |
| Aus | 269 | 1.90% | 0.00% | 1.49% | 96.65% | NA |
| Indica I | 595 | 7.70% | 0.00% | 3.03% | 89.24% | NA |
| Indica II | 465 | 3.70% | 0.00% | 3.01% | 93.33% | NA |
| Indica III | 913 | 3.10% | 0.00% | 5.15% | 91.79% | NA |
| Indica Intermediate | 786 | 3.70% | 0.10% | 5.22% | 90.97% | NA |
| Temperate Japonica | 767 | 74.10% | 15.00% | 0.13% | 10.82% | NA |
| Tropical Japonica | 504 | 9.30% | 0.00% | 0.79% | 89.88% | NA |
| Japonica Intermediate | 241 | 54.40% | 0.40% | 0.83% | 44.40% | NA |
| VI/Aromatic | 96 | 7.30% | 0.00% | 1.04% | 91.67% | NA |
| Intermediate | 90 | 25.60% | 1.10% | 4.44% | 68.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1006628058 | A -> G | LOC_Os10g11954.1 | missense_variant ; p.Ile341Val; MODERATE | nonsynonymous_codon ; I341V | Average:8.525; most accessible tissue: Minghui63 root, score: 17.665 | benign  |
-0.137 |
TOLERATED | 1.00 |
| vg1006628058 | A -> DEL | LOC_Os10g11954.1 | N | frameshift_variant | Average:8.525; most accessible tissue: Minghui63 root, score: 17.665 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1006628058 | 8.91E-07 | 8.91E-07 | mr1267_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 |