Search for Variation information by Variation ID:
Detailed information for vg0615088161:
| Variant ID: vg0615088161 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 15088161 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AGCTTCATTTGGAGATGAGTGAATGCTAGGAATGTCTTCATTAACTAGTCGGCGGCGGACGAGGCAGCCGGTCGGTGAGGATGTAGACGCCCAACAACGG[C/T]
GGCATAATAGGCCAGCCATGCAGGCGGAAACACCAGTCGGCGGCGGACGAGGCGACCGGTCGGTGAAGACGTAGACGCTCAACAACAGTGGCATAATAGG
Reverse complement sequence
CCTATTATGCCACTGTTGTTGAGCGTCTACGTCTTCACCGACCGGTCGCCTCGTCCGCCGCCGACTGGTGTTTCCGCCTGCATGGCTGGCCTATTATGCC[G/A]
CCGTTGTTGGGCGTCTACATCCTCACCGACCGGCTGCCTCGTCCGCCGCCGACTAGTTAATGAAGACATTCCTAGCATTCACTCATCTCCAAATGAAGCT
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 | 88.80% | 4.50% | 1.80% | 4.89% | NA |
| All Indica | 2759 | 89.60% | 7.20% | 2.94% | 0.25% | NA |
| All Japonica | 1512 | 99.70% | 0.10% | 0.00% | 0.13% | NA |
| Aus | 269 | 33.80% | 4.10% | 0.37% | 61.71% | NA |
| Indica I | 595 | 89.20% | 7.10% | 3.70% | 0.00% | NA |
| Indica II | 465 | 88.80% | 6.70% | 4.52% | 0.00% | NA |
| Indica III | 913 | 93.30% | 5.80% | 0.77% | 0.11% | NA |
| Indica Intermediate | 786 | 85.90% | 9.40% | 3.94% | 0.76% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.20% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 44.80% | 2.10% | 3.12% | 50.00% | NA |
| Intermediate | 90 | 91.10% | 0.00% | 0.00% | 8.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0615088161 | C -> T | LOC_Os06g25830.1 | missense_variant ; p.Arg170His; MODERATE | nonsynonymous_codon ; R170H | Average:34.298; most accessible tissue: Minghui63 panicle, score: 59.629 | benign  |
0.707 |
TOLERATED | 0.20 |
| vg0615088161 | C -> DEL | LOC_Os06g25830.1 | N | frameshift_variant | Average:34.298; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0615088161 | 2.80E-06 | 2.80E-06 | mr1875 | 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 |