Search for Variation information by Variation ID:
Detailed information for vg0401290717:
| Variant ID: vg0401290717 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 1290717 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AGCTGTCGGAATTCCTCCGAGTCCGACCTCCCACTTTTTCAAGCACAACCAATCCCGTCGAAGCAAATGACTGGCTGCACGCGGTTAACAAGAAATTGGA[C/A]
CTCATCCAATGTACTGATGAAGAGAAAGTCGCCTTCGCCGCTCACCAACTGCATGGACCTGCTTCCGAGTGGTGGGACCATTTCCAAGCCACCCAGCCAG
Reverse complement sequence
CTGGCTGGGTGGCTTGGAAATGGTCCCACCACTCGGAAGCAGGTCCATGCAGTTGGTGAGCGGCGAAGGCGACTTTCTCTTCATCAGTACATTGGATGAG[G/T]
TCCAATTTCTTGTTAACCGCGTGCAGCCAGTCATTTGCTTCGACGGGATTGGTTGTGCTTGAAAAAGTGGGAGGTCGGACTCGGAGGAATTCCGACAGCT
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 | 76.70% | 3.50% | 1.61% | 18.24% | NA |
| All Indica | 2759 | 99.30% | 0.10% | 0.18% | 0.36% | NA |
| All Japonica | 1512 | 41.00% | 0.00% | 3.17% | 55.82% | NA |
| Aus | 269 | 35.70% | 57.60% | 6.69% | 0.00% | NA |
| Indica I | 595 | 99.70% | 0.00% | 0.00% | 0.34% | NA |
| Indica II | 465 | 99.10% | 0.00% | 0.22% | 0.65% | NA |
| Indica III | 913 | 99.70% | 0.00% | 0.33% | 0.00% | NA |
| Indica Intermediate | 786 | 98.90% | 0.40% | 0.13% | 0.64% | NA |
| Temperate Japonica | 767 | 56.50% | 0.00% | 1.96% | 41.59% | NA |
| Tropical Japonica | 504 | 25.60% | 0.00% | 5.75% | 68.65% | NA |
| Japonica Intermediate | 241 | 24.10% | 0.00% | 1.66% | 74.27% | NA |
| VI/Aromatic | 96 | 93.80% | 4.20% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 84.40% | 3.30% | 5.56% | 6.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0401290717 | C -> DEL | LOC_Os04g03110.1 | N | frameshift_variant | Average:23.133; most accessible tissue: Callus, score: 49.758 | N | N | N | N |
| vg0401290717 | C -> A | LOC_Os04g03110.1 | missense_variant ; p.Asp75Glu; MODERATE | nonsynonymous_codon ; D75E | Average:23.133; most accessible tissue: Callus, score: 49.758 | benign  |
0.539 |
DELETERIOUS | 0.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0401290717 | NA | 4.80E-06 | mr1345 | 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 |
| vg0401290717 | NA | 7.47E-06 | mr1427 | 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 |
| vg0401290717 | NA | 6.08E-13 | mr1522 | 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 |
| vg0401290717 | NA | 4.00E-06 | mr1523 | 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 |
| vg0401290717 | NA | 1.20E-06 | mr1787 | 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 |
| vg0401290717 | NA | 5.58E-08 | mr1510_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 |