Search for Variation information by Variation ID:
Detailed information for vg0614462670:
| Variant ID: vg0614462670 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 14462670 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CCAGCTACGGCCCCATGAAGGCAACTATCCTACTCATGATTTGGAGTTGGCCGCTGTGGTTCATGATTTGAAAATCTGGCGGCATTATCTCATTGGAAAT[C/A]
GCTGCGAAATATATACCGATCATAAGAGTTTGAAATACATCTTCACTCAGTCAGATCTGAATCTTCAGCAGAGAAGATGGTTAGAGCTCATCAAAGATTA
Reverse complement sequence
TAATCTTTGATGAGCTCTAACCATCTTCTCTGCTGAAGATTCAGATCTGACTGAGTGAAGATGTATTTCAAACTCTTATGATCGGTATATATTTCGCAGC[G/T]
ATTTCCAATGAGATAATGCCGCCAGATTTTCAAATCATGAACCACAGCGGCCAACTCCAAATCATGAGTAGGATAGTTGCCTTCATGGGGCCGTAGCTGG
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 89.90% | 1.30% | 4.76% | 4.08% | NA |
| All Indica | 2759 | 87.90% | 2.00% | 7.18% | 2.90% | NA |
| All Japonica | 1512 | 93.20% | 0.00% | 0.66% | 6.15% | NA |
| Aus | 269 | 91.40% | 1.10% | 4.83% | 2.60% | NA |
| Indica I | 595 | 90.10% | 0.70% | 5.38% | 3.87% | NA |
| Indica II | 465 | 82.60% | 2.20% | 12.90% | 2.37% | NA |
| Indica III | 913 | 89.40% | 2.50% | 5.48% | 2.63% | NA |
| Indica Intermediate | 786 | 87.70% | 2.40% | 7.12% | 2.80% | NA |
| Temperate Japonica | 767 | 98.20% | 0.00% | 0.52% | 1.30% | NA |
| Tropical Japonica | 504 | 84.70% | 0.00% | 0.79% | 14.48% | NA |
| Japonica Intermediate | 241 | 95.00% | 0.00% | 0.83% | 4.15% | NA |
| VI/Aromatic | 96 | 91.70% | 0.00% | 0.00% | 8.33% | NA |
| Intermediate | 90 | 88.90% | 1.10% | 4.44% | 5.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0614462670 | C -> A | LOC_Os06g24630.1 | missense_variant ; p.Arg602Ser; MODERATE | nonsynonymous_codon ; R602S | Average:11.243; most accessible tissue: Callus, score: 19.299 | benign  |
0.701 |
DELETERIOUS | 0.01 |
| vg0614462670 | C -> DEL | LOC_Os06g24630.1 | N | frameshift_variant | Average:11.243; most accessible tissue: Callus, score: 19.299 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0614462670 | NA | 1.24E-07 | mr1004 | 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 |
| vg0614462670 | 9.69E-06 | 5.58E-08 | mr1005 | 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 |
| vg0614462670 | NA | 2.80E-06 | mr1018 | 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 |