Search for Variation information by Variation ID:
Detailed information for vg0716573684:
| Variant ID: vg0716573684 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 16573684 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 322. )
Flanking Sequence (100 bp) in Reference Genome:
CGCTTGGAAGCACAAGATGAAGTTGCATTTAATCTCGTTGCATCCAAGTATTTGGAAAGTTGTTTGTACAGGTATTGATGTACCCCATGATGACATGGAG[C/T]
TCACCTCGGAGCAAGAGCAACTCATCCACTGCAATGCTCAAGCTTCCAATGCAATTCTCTCTGCCTTGAGTCTGGAGGAGTTCAACAAGGTTGATGGACT
Reverse complement sequence
AGTCCATCAACCTTGTTGAACTCCTCCAGACTCAAGGCAGAGAGAATTGCATTGGAAGCTTGAGCATTGCAGTGGATGAGTTGCTCTTGCTCCGAGGTGA[G/A]
CTCCATGTCATCATGGGGTACATCAATACCTGTACAAACAACTTTCCAAATACTTGGATGCAACGAGATTAAATGCAACTTCATCTTGTGCTTCCAAGCG
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 | 89.70% | 8.30% | 0.28% | 1.71% | NA |
| All Indica | 2759 | 82.60% | 14.00% | 0.47% | 2.94% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 71.80% | 24.50% | 0.67% | 3.03% | NA |
| Indica II | 465 | 97.60% | 2.20% | 0.00% | 0.22% | NA |
| Indica III | 913 | 82.70% | 12.60% | 0.33% | 4.38% | NA |
| Indica Intermediate | 786 | 81.90% | 14.50% | 0.76% | 2.80% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 5.60% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0716573684 | C -> DEL | LOC_Os07g28370.1 | N | frameshift_variant | Average:41.299; most accessible tissue: Zhenshan97 flag leaf, score: 61.926 | N | N | N | N |
| vg0716573684 | C -> T | LOC_Os07g28370.1 | missense_variant ; p.Leu94Phe; MODERATE | nonsynonymous_codon ; L94F | Average:41.299; most accessible tissue: Zhenshan97 flag leaf, score: 61.926 | probably damaging  |
2.145 |
TOLERATED | 0.10 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0716573684 | NA | 3.05E-06 | mr1970 | 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 |
| vg0716573684 | NA | 3.76E-07 | mr1648_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 |
| vg0716573684 | NA | 3.70E-08 | mr1648_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 |
| vg0716573684 | NA | 1.68E-06 | mr1655_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 |
| vg0716573684 | NA | 3.29E-06 | mr1669_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 |
| vg0716573684 | NA | 1.12E-07 | mr1970_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 |