Search for Variation information by Variation ID:
Detailed information for vg0413762842:
| Variant ID: vg0413762842 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 13762842 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.56, T: 0.44, others allele: 0.00, population size: 86. )
Flanking Sequence (100 bp) in Reference Genome:
ATCTCCCGGATTTGAGACAAACCGGCTCAGCTTGCTTACAGCAAATGAGATGTCAGGCCTCGTTGCACTAGCCAAGTACATCAATGAACCAATGATTTGA[T/G]
AGTATCTCAGTTGATCCCTTGCTATTCTTCGGTTTTTCCTTAATAGCACACTGGGATCATAAGGAGTAGGAGTTGGCTTGCAGTCACTATATCCAAAGCA
Reverse complement sequence
TGCTTTGGATATAGTGACTGCAAGCCAACTCCTACTCCTTATGATCCCAGTGTGCTATTAAGGAAAAACCGAAGAATAGCAAGGGATCAACTGAGATACT[A/C]
TCAAATCATTGGTTCATTGATGTACTTGGCTAGTGCAACGAGGCCTGACATCTCATTTGCTGTAAGCAAGCTGAGCCGGTTTGTCTCAAATCCGGGAGAT
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 46.80% | 22.20% | 28.18% | 2.86% | NA |
| All Indica | 2759 | 27.70% | 34.80% | 35.77% | 1.74% | NA |
| All Japonica | 1512 | 90.80% | 0.40% | 4.43% | 4.37% | NA |
| Aus | 269 | 7.40% | 22.30% | 70.26% | 0.00% | NA |
| Indica I | 595 | 56.10% | 12.10% | 25.88% | 5.88% | NA |
| Indica II | 465 | 8.00% | 56.80% | 35.05% | 0.22% | NA |
| Indica III | 913 | 16.80% | 39.90% | 43.37% | 0.00% | NA |
| Indica Intermediate | 786 | 30.50% | 33.10% | 34.86% | 1.53% | NA |
| Temperate Japonica | 767 | 98.20% | 0.10% | 0.26% | 1.43% | NA |
| Tropical Japonica | 504 | 86.50% | 0.40% | 7.34% | 5.75% | NA |
| Japonica Intermediate | 241 | 76.30% | 1.20% | 11.62% | 10.79% | NA |
| VI/Aromatic | 96 | 15.60% | 4.20% | 62.50% | 17.71% | NA |
| Intermediate | 90 | 44.40% | 18.90% | 32.22% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0413762842 | T -> DEL | LOC_Os04g24100.1 | N | frameshift_variant | Average:22.394; most accessible tissue: Zhenshan97 flag leaf, score: 49.013 | N | N | N | N |
| vg0413762842 | T -> G | LOC_Os04g24100.1 | missense_variant ; p.Tyr1014Ser; MODERATE | nonsynonymous_codon ; Y1014S | Average:22.394; most accessible tissue: Zhenshan97 flag leaf, score: 49.013 | benign  |
-0.636 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0413762842 | NA | 1.24E-06 | mr1866 | Jap_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 |
| vg0413762842 | 2.92E-07 | 2.23E-10 | mr1350_2 | Jap_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 |
| vg0413762842 | 3.09E-06 | NA | mr1584_2 | Jap_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 |
| vg0413762842 | 6.11E-06 | NA | mr1730_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 |
| vg0413762842 | 4.43E-07 | 6.72E-08 | mr1730_2 | Jap_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 |
| vg0413762842 | 4.80E-06 | 2.32E-15 | mr1866_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 |