Search for Variation information by Variation ID:
Detailed information for vg0408189411:
| Variant ID: vg0408189411 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 8189411 |
| Reference Allele: G | Alternative Allele: C,A |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 105. )
Flanking Sequence (100 bp) in Reference Genome:
CACACCCACAATCAAACGGGGCGGCCGAACGCACAAACGGCAAAATCCTAGAAGCACTAAAGAAAAGGCTCGAGGGGGCAGCGAAGGGCAAATGGCCAGA[G/C,A]
GAAATGCTGTCTGTTCTCTGGGCCCTTCGAACGACCCGTACAAGACCAACCAAGTTCAGCCCGTTCATGCTACTTTTTGGCGATGAAGCAATGACCCCAA
Reverse complement sequence
TTGGGGTCATTGCTTCATCGCCAAAAAGTAGCATGAACGGGCTGAACTTGGTTGGTCTTGTACGGGTCGTTCGAAGGGCCCAGAGAACAGACAGCATTTC[C/G,T]
TCTGGCCATTTGCCCTTCGCTGCCCCCTCGAGCCTTTTCTTTAGTGCTTCTAGGATTTTGCCGTTTGTGCGTTCGGCCGCCCCGTTTGATTGTGGGTGTG
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 43.70% | 33.50% | 5.46% | 17.29% | A: 0.06% |
| All Indica | 2759 | 34.50% | 54.80% | 4.42% | 6.23% | NA |
| All Japonica | 1512 | 66.70% | 0.70% | 3.57% | 28.97% | A: 0.07% |
| Aus | 269 | 20.10% | 14.10% | 17.47% | 48.33% | NA |
| Indica I | 595 | 27.70% | 65.50% | 2.86% | 3.87% | NA |
| Indica II | 465 | 47.50% | 35.30% | 6.67% | 10.54% | NA |
| Indica III | 913 | 37.90% | 55.20% | 2.63% | 4.27% | NA |
| Indica Intermediate | 786 | 28.10% | 57.80% | 6.36% | 7.76% | NA |
| Temperate Japonica | 767 | 96.60% | 0.30% | 0.13% | 3.00% | NA |
| Tropical Japonica | 504 | 18.80% | 1.20% | 9.33% | 70.44% | A: 0.20% |
| Japonica Intermediate | 241 | 71.40% | 1.20% | 2.49% | 24.90% | NA |
| VI/Aromatic | 96 | 16.70% | 4.20% | 25.00% | 54.17% | NA |
| Intermediate | 90 | 40.00% | 17.80% | 12.22% | 27.78% | A: 2.22% |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0408189411 | G -> C | LOC_Os04g14590.1 | missense_variant ; p.Glu726Asp; MODERATE | nonsynonymous_codon ; E726D | Average:32.279; most accessible tissue: Minghui63 root, score: 43.505 | benign  |
-0.028 |
TOLERATED | 0.24 |
| vg0408189411 | G -> DEL | LOC_Os04g14590.1 | N | frameshift_variant | Average:32.279; most accessible tissue: Minghui63 root, score: 43.505 | N | N | N | N |
| vg0408189411 | G -> A | LOC_Os04g14590.1 | synonymous_variant ; p.Glu726Glu; LOW | synonymous_codon | Average:32.279; most accessible tissue: Minghui63 root, score: 43.505 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0408189411 | NA | 2.80E-06 | mr1525 | 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 |
| vg0408189411 | NA | 2.02E-06 | mr1720 | 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 |
| vg0408189411 | NA | 6.50E-06 | mr1817 | 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 |
| vg0408189411 | 3.45E-06 | NA | mr1224_2 | 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 |