Search for Variation information by Variation ID:
Detailed information for vg0816201029:
| Variant ID: vg0816201029 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 16201029 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GAGTATGTGCTTCTTCAACATTTCCATACGGGTTTGGATAAAGAGTCTGCATTCTATCTGGACATAACCGTTGGAGGATTGTTCATGCACAAAACGCCGT[C/T]
AGAAGGAAGAACAATTTTGGATCACATTCTAGAAAATACTTCCTTCATGACGCAATCAATTGAACCCCAGCCGGAGGCATCCGTGTCCAAGATAGAGGAA
Reverse complement sequence
TTCCTCTATCTTGGACACGGATGCCTCCGGCTGGGGTTCAATTGATTGCGTCATGAAGGAAGTATTTTCTAGAATGTGATCCAAAATTGTTCTTCCTTCT[G/A]
ACGGCGTTTTGTGCATGAACAATCCTCCAACGGTTATGTCCAGATAGAATGCAGACTCTTTATCCAAACCCGTATGGAAATGTTGAAGAAGCACATACTC
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 | 50.50% | 0.30% | 13.29% | 35.95% | NA |
| All Indica | 2759 | 38.20% | 0.40% | 20.55% | 40.85% | NA |
| All Japonica | 1512 | 70.80% | 0.10% | 1.39% | 27.78% | NA |
| Aus | 269 | 41.60% | 0.00% | 10.04% | 48.33% | NA |
| Indica I | 595 | 27.20% | 0.50% | 13.61% | 58.66% | NA |
| Indica II | 465 | 44.50% | 0.60% | 21.29% | 33.55% | NA |
| Indica III | 913 | 39.80% | 0.70% | 23.55% | 36.04% | NA |
| Indica Intermediate | 786 | 40.80% | 0.00% | 21.88% | 37.28% | NA |
| Temperate Japonica | 767 | 98.00% | 0.00% | 0.13% | 1.83% | NA |
| Tropical Japonica | 504 | 27.60% | 0.20% | 3.57% | 68.65% | NA |
| Japonica Intermediate | 241 | 74.30% | 0.00% | 0.83% | 24.90% | NA |
| VI/Aromatic | 96 | 93.80% | 0.00% | 3.12% | 3.12% | NA |
| Intermediate | 90 | 67.80% | 0.00% | 11.11% | 21.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0816201029 | C -> T | LOC_Os08g26650.1 | missense_variant ; p.Ser179Leu; MODERATE | nonsynonymous_codon ; S179L | Average:14.399; most accessible tissue: Callus, score: 44.201 | benign  |
0.42 |
TOLERATED | 0.14 |
| vg0816201029 | C -> DEL | LOC_Os08g26650.1 | N | frameshift_variant | Average:14.399; most accessible tissue: Callus, score: 44.201 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0816201029 | 2.62E-06 | 2.62E-06 | mr1081_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 |
| vg0816201029 | NA | 2.10E-06 | mr1123_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 |
| vg0816201029 | NA | 2.28E-06 | mr1496_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 |
| vg0816201029 | NA | 7.55E-07 | mr1936_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 |