Search for Variation information by Variation ID:
Detailed information for vg0708117804:
| Variant ID: vg0708117804 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 8117804 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, T: 0.04, others allele: 0.00, population size: 109. )
Flanking Sequence (100 bp) in Reference Genome:
AATCTGTCAGGAGGATCAGCGAAATAAAATGGACAGGAAGAGAAAGGCGGCACAGTTCCGGTCCAACCAAGGAAACCATCAGCGACCGCGCTTCGCTCCC[G/T]
GGCAGCAGGGTGGACCTACCACCATGATCGTCCGCCAGTACCGCCCGTTCAACTCTAGCAACTTCCACCAGGGCGCCAGTGGCAGTCAGAACCACCATGG
Reverse complement sequence
CCATGGTGGTTCTGACTGCCACTGGCGCCCTGGTGGAAGTTGCTAGAGTTGAACGGGCGGTACTGGCGGACGATCATGGTGGTAGGTCCACCCTGCTGCC[C/A]
GGGAGCGAAGCGCGGTCGCTGATGGTTTCCTTGGTTGGACCGGAACTGTGCCGCCTTTCTCTTCCTGTCCATTTTATTTCGCTGATCCTCCTGACAGATT
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 36.90% | 35.50% | 5.65% | 21.88% | NA |
| All Indica | 2759 | 4.50% | 58.40% | 6.67% | 30.48% | NA |
| All Japonica | 1512 | 88.20% | 0.30% | 0.33% | 11.18% | NA |
| Aus | 269 | 62.10% | 14.90% | 22.30% | 0.74% | NA |
| Indica I | 595 | 2.90% | 12.40% | 5.88% | 78.82% | NA |
| Indica II | 465 | 7.70% | 74.60% | 7.96% | 9.68% | NA |
| Indica III | 913 | 3.90% | 76.60% | 7.01% | 12.49% | NA |
| Indica Intermediate | 786 | 4.50% | 62.30% | 6.11% | 27.10% | NA |
| Temperate Japonica | 767 | 85.00% | 0.50% | 0.26% | 14.21% | NA |
| Tropical Japonica | 504 | 89.50% | 0.20% | 0.20% | 10.12% | NA |
| Japonica Intermediate | 241 | 95.40% | 0.00% | 0.83% | 3.73% | NA |
| VI/Aromatic | 96 | 76.00% | 5.20% | 10.42% | 8.33% | NA |
| Intermediate | 90 | 53.30% | 22.20% | 8.89% | 15.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0708117804 | G -> DEL | LOC_Os07g14250.1 | N | frameshift_variant | Average:16.963; most accessible tissue: Minghui63 young leaf, score: 29.964 | N | N | N | N |
| vg0708117804 | G -> T | LOC_Os07g14250.1 | missense_variant ; p.Gly287Trp; MODERATE | nonsynonymous_codon ; G287W | Average:16.963; most accessible tissue: Minghui63 young leaf, score: 29.964 | probably damaging  |
3.497 |
DELETERIOUS | 0.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0708117804 | NA | 2.06E-22 | mr1083 | 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 |
| vg0708117804 | 5.21E-06 | NA | mr1508_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 |