Search for Variation information by Variation ID:
Detailed information for vg0122178298:
| Variant ID: vg0122178298 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 22178298 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.93, T: 0.07, others allele: 0.00, population size: 286. )
Flanking Sequence (100 bp) in Reference Genome:
CGGCATGAGGAAGCCATTCTTTTGGAGGAGCCTCCACAGAAAGAAGGCAATTCTCAATGGCAAATAAAACACGATTCTTTCCTGGTGTTGGTAATGGAAC[T/A]
TTTGACACCAAATGTGATATTATGTCCCACAATGGCTTGCTGAAATCAGAGCACACAAAAATTAGACCATAAGAAGGTTCCAACCAGAATATACAACTTG
Reverse complement sequence
CAAGTTGTATATTCTGGTTGGAACCTTCTTATGGTCTAATTTTTGTGTGCTCTGATTTCAGCAAGCCATTGTGGGACATAATATCACATTTGGTGTCAAA[A/T]
GTTCCATTACCAACACCAGGAAAGAATCGTGTTTTATTTGCCATTGAGAATTGCCTTCTTTCTGTGGAGGCTCCTCCAAAAGAATGGCTTCCTCATGCCG
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 55.40% | 44.60% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 87.00% | 13.00% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 0.30% | 99.70% | 0.00% | 0.00% | NA |
| Aus | 269 | 62.10% | 37.90% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 93.10% | 6.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 78.40% | 21.60% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 83.30% | 16.50% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 0.10% | 99.90% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 0.40% | 99.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 0.80% | 99.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 10.40% | 89.60% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 38.90% | 60.00% | 1.11% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0122178298 | T -> A | LOC_Os01g39380.1 | missense_variant ; p.Lys171Asn; MODERATE | nonsynonymous_codon ; K171N | Average:46.911; most accessible tissue: Callus, score: 80.424 | benign  |
-0.466 |
TOLERATED | 1.00 |
| vg0122178298 | T -> A | LOC_Os01g39380.2 | missense_variant ; p.Lys171Asn; MODERATE | nonsynonymous_codon ; K171N | Average:46.911; most accessible tissue: Callus, score: 80.424 | benign |
-0.466 |
TOLERATED | 1.00 |
| vg0122178298 | T -> A | LOC_Os01g39380.3 | missense_variant ; p.Lys171Asn; MODERATE | nonsynonymous_codon ; K171N | Average:46.911; most accessible tissue: Callus, score: 80.424 | benign |
-0.478 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0122178298 | NA | 3.64E-21 | mr1003 | 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 |
| vg0122178298 | NA | 1.23E-10 | mr1281 | 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 |
| vg0122178298 | NA | 2.29E-20 | mr1580 | 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 |
| vg0122178298 | NA | 8.40E-42 | mr1591 | 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 |
| vg0122178298 | NA | 5.13E-28 | mr1051_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 |
| vg0122178298 | NA | 2.78E-08 | mr1080_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 |
| vg0122178298 | NA | 4.12E-08 | mr1203_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 |
| vg0122178298 | NA | 7.98E-22 | mr1609_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 |
| vg0122178298 | NA | 1.48E-07 | mr1619_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 |