Search for Variation information by Variation ID:
Detailed information for vg0714251118:
| Variant ID: vg0714251118 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 14251118 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 36. )
Flanking Sequence (100 bp) in Reference Genome:
AACCTCCCTGTGGCATGGACAGGGGTCCCGAAGCAATACGCGGCCTCTGACTATTTCCCTGCTGTGCCTTGAAGTGAGCAATCCGGTGTTTCTTCTGCTC[C/G]
ATGCGATTATAATTGTCCTCCTGACGAATAGCCTTATCCACTAACTTCTGGAAATCGTGATAATCTCCAGTCATGAGTGGGTAAGAAAGCTCATCATTAA
Reverse complement sequence
TTAATGATGAGCTTTCTTACCCACTCATGACTGGAGATTATCACGATTTCCAGAAGTTAGTGGATAAGGCTATTCGTCAGGAGGACAATTATAATCGCAT[G/C]
GAGCAGAAGAAACACCGGATTGCTCACTTCAAGGCACAGCAGGGAAATAGTCAGAGGCCGCGTATTGCTTCGGGACCCCTGTCCATGCCACAGGGAGGTT
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 49.30% | 17.20% | 6.83% | 26.72% | NA |
| All Indica | 2759 | 35.90% | 27.80% | 4.68% | 31.64% | NA |
| All Japonica | 1512 | 70.90% | 2.20% | 10.12% | 16.73% | NA |
| Aus | 269 | 45.70% | 1.10% | 12.64% | 40.52% | NA |
| Indica I | 595 | 47.10% | 17.00% | 2.18% | 33.78% | NA |
| Indica II | 465 | 35.50% | 35.10% | 9.46% | 20.00% | NA |
| Indica III | 913 | 24.60% | 31.00% | 3.94% | 40.42% | NA |
| Indica Intermediate | 786 | 40.80% | 27.90% | 4.58% | 26.72% | NA |
| Temperate Japonica | 767 | 70.90% | 0.10% | 15.12% | 13.82% | NA |
| Tropical Japonica | 504 | 72.20% | 6.30% | 1.59% | 19.84% | NA |
| Japonica Intermediate | 241 | 68.00% | 0.40% | 12.03% | 19.50% | NA |
| VI/Aromatic | 96 | 84.40% | 1.00% | 3.12% | 11.46% | NA |
| Intermediate | 90 | 67.80% | 8.90% | 4.44% | 18.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0714251118 | C -> DEL | LOC_Os07g25010.1 | N | frameshift_variant | Average:8.647; most accessible tissue: Callus, score: 41.635 | N | N | N | N |
| vg0714251118 | C -> G | LOC_Os07g25010.1 | missense_variant ; p.Met455Ile; MODERATE | nonsynonymous_codon ; M455I | Average:8.647; most accessible tissue: Callus, score: 41.635 | benign  |
-0.019 |
DELETERIOUS | 0.05 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0714251118 | 1.09E-06 | 1.03E-10 | mr1053 | 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 |
| vg0714251118 | 7.41E-07 | 6.78E-08 | mr1053 | 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 |
| vg0714251118 | 7.08E-07 | NA | mr1128 | 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 |
| vg0714251118 | 1.76E-07 | 8.33E-08 | mr1128 | 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 |
| vg0714251118 | 7.55E-06 | 4.51E-06 | mr1147 | 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 |
| vg0714251118 | NA | 2.39E-08 | mr1709 | 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 |
| vg0714251118 | NA | 8.79E-06 | mr1027_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 |
| vg0714251118 | NA | 7.68E-08 | mr1053_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 |
| vg0714251118 | NA | 3.66E-06 | mr1053_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 |