Search for Variation information by Variation ID:
Detailed information for vg0714101037:
| Variant ID: vg0714101037 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 14101037 |
| Reference Allele: G | Alternative Allele: C |
| 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:
CATTTTTTGTCATGTGACATGAGCCTGTCGTAGACGCGGGTTTTGATCCCTTGTAGTACTATGCTGTTTGCCCTCTCGACTTGTCCGTTGCTTTGAGGGT[G/C]
AGAGACCGAGGCGAAGCATATCTTGACTCCCAGCCCGATGTAGTAATCCTGAAAATCAGCGCTGATGAACTGGGAGCCGTTGTCGGTTATGATGGGGTGC
Reverse complement sequence
GCACCCCATCATAACCGACAACGGCTCCCAGTTCATCAGCGCTGATTTTCAGGATTACTACATCGGGCTGGGAGTCAAGATATGCTTCGCCTCGGTCTCT[C/G]
ACCCTCAAAGCAACGGACAAGTCGAGAGGGCAAACAGCATAGTACTACAAGGGATCAAAACCCGCGTCTACGACAGGCTCATGTCACATGACAAAAAATG
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 | 75.90% | 2.90% | 16.97% | 4.19% | NA |
| All Indica | 2759 | 66.30% | 3.60% | 26.71% | 3.48% | NA |
| All Japonica | 1512 | 89.20% | 2.20% | 2.05% | 6.55% | NA |
| Aus | 269 | 87.40% | 1.10% | 10.41% | 1.12% | NA |
| Indica I | 595 | 77.00% | 1.30% | 20.50% | 1.18% | NA |
| Indica II | 465 | 70.50% | 4.50% | 21.29% | 3.66% | NA |
| Indica III | 913 | 59.30% | 3.80% | 32.09% | 4.82% | NA |
| Indica Intermediate | 786 | 63.70% | 4.30% | 28.37% | 3.56% | NA |
| Temperate Japonica | 767 | 90.50% | 0.30% | 2.22% | 7.04% | NA |
| Tropical Japonica | 504 | 94.80% | 1.60% | 1.59% | 1.98% | NA |
| Japonica Intermediate | 241 | 73.00% | 10.00% | 2.49% | 14.52% | NA |
| VI/Aromatic | 96 | 97.90% | 1.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 2.20% | 5.56% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0714101037 | G -> DEL | LOC_Os07g24810.1 | N | frameshift_variant | Average:10.599; most accessible tissue: Callus, score: 32.808 | N | N | N | N |
| vg0714101037 | G -> C | LOC_Os07g24810.1 | missense_variant ; p.His708Asp; MODERATE | nonsynonymous_codon ; H708D | Average:10.599; most accessible tissue: Callus, score: 32.808 | possibly damaging  |
1.891 |
DELETERIOUS | 0.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0714101037 | NA | 1.09E-06 | mr1252 | 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 |