Search for Variation information by Variation ID:
Detailed information for vg0403437872:
| Variant ID: vg0403437872 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 3437872 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.64, T: 0.35, others allele: 0.00, population size: 62. )
Flanking Sequence (100 bp) in Reference Genome:
CTTCAACAAGATGATAGAGATACAGCTGGCACAGTTAGCTGCTCTAGTCGCTACAAATGAGTCTAGGAGGATTCTAGGACAACCCGAACCTTCCTTAGAG[T/C]
ATGTTAAGGCGATCACCATGAGCCGGGGAAAGTCTACTCGGGATCCGCCATATCCTAACCCTGCAGGAACACAGAGCAGTAACAAGGAGGCATCACCTGC
Reverse complement sequence
GCAGGTGATGCCTCCTTGTTACTGCTCTGTGTTCCTGCAGGGTTAGGATATGGCGGATCCCGAGTAGACTTTCCCCGGCTCATGGTGATCGCCTTAACAT[A/G]
CTCTAAGGAAGGTTCGGGTTGTCCTAGAATCCTCCTAGACTCATTTGTAGCGACTAGAGCAGCTAACTGTGCCAGCTGTATCTCTATCATCTTGTTGAAG
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 | 26.40% | 20.30% | 0.57% | 52.69% | NA |
| All Indica | 2759 | 29.10% | 3.60% | 0.80% | 66.44% | NA |
| All Japonica | 1512 | 17.00% | 45.40% | 0.26% | 37.30% | NA |
| Aus | 269 | 42.40% | 54.60% | 0.00% | 2.97% | NA |
| Indica I | 595 | 4.40% | 5.70% | 0.34% | 89.58% | NA |
| Indica II | 465 | 40.40% | 4.30% | 1.51% | 53.76% | NA |
| Indica III | 913 | 37.00% | 1.20% | 0.55% | 61.23% | NA |
| Indica Intermediate | 786 | 32.10% | 4.50% | 1.02% | 62.47% | NA |
| Temperate Japonica | 767 | 10.40% | 77.20% | 0.39% | 11.99% | NA |
| Tropical Japonica | 504 | 21.60% | 9.50% | 0.00% | 68.85% | NA |
| Japonica Intermediate | 241 | 28.20% | 19.50% | 0.41% | 51.87% | NA |
| VI/Aromatic | 96 | 50.00% | 6.20% | 0.00% | 43.75% | NA |
| Intermediate | 90 | 30.00% | 21.10% | 1.11% | 47.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0403437872 | T -> C | LOC_Os04g06540.1 | missense_variant ; p.Tyr183His; MODERATE | nonsynonymous_codon ; Y183H | Average:39.741; most accessible tissue: Zhenshan97 young leaf, score: 73.923 | benign  |
-0.158 |
TOLERATED | 0.06 |
| vg0403437872 | T -> DEL | LOC_Os04g06540.1 | N | frameshift_variant | Average:39.741; most accessible tissue: Zhenshan97 young leaf, score: 73.923 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0403437872 | NA | 4.95E-08 | mr1403 | 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 |
| vg0403437872 | NA | 4.92E-06 | mr1576 | 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 |
| vg0403437872 | NA | 4.47E-12 | mr1763 | 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 |
| vg0403437872 | NA | 2.11E-07 | mr1804 | 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 |