Search for Variation information by Variation ID:
Detailed information for vg0401439086:
| Variant ID: vg0401439086 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 1439086 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CGACGTATTCCCGAAGCTAAGGGATCATTGGGACGAGTTCGCTGCTTACAAGACAGGGCAACAAGGGCAAGCGATGATGGTCAGAAACAAAGAAAATGCC[G/A]
CCAAGAAGAAGTACCATCACCACTTGGGGTCAGGCGGCTGTAGCGTCGCAATGCCGAATTGCGAGGAGATGGAGGCAAGCTTGATTGAGAGGGGTATCGA
Reverse complement sequence
TCGATACCCCTCTCAATCAAGCTTGCCTCCATCTCCTCGCAATTCGGCATTGCGACGCTACAGCCGCCTGACCCCAAGTGGTGATGGTACTTCTTCTTGG[C/T]
GGCATTTTCTTTGTTTCTGACCATCATCGCTTGCCCTTGTTGCCCTGTCTTGTAAGCAGCGAACTCGTCCCAATGATCCCTTAGCTTCGGGAATACGTCG
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 30.00% | 0.30% | 58.97% | 10.69% | NA |
| All Indica | 2759 | 23.20% | 0.40% | 67.27% | 9.21% | NA |
| All Japonica | 1512 | 47.10% | 0.00% | 40.01% | 12.90% | NA |
| Aus | 269 | 11.90% | 1.50% | 83.64% | 2.97% | NA |
| Indica I | 595 | 47.10% | 1.20% | 40.17% | 11.60% | NA |
| Indica II | 465 | 20.90% | 0.00% | 70.54% | 8.60% | NA |
| Indica III | 913 | 9.60% | 0.00% | 82.58% | 7.78% | NA |
| Indica Intermediate | 786 | 22.10% | 0.40% | 68.07% | 9.41% | NA |
| Temperate Japonica | 767 | 70.90% | 0.00% | 9.13% | 19.95% | NA |
| Tropical Japonica | 504 | 14.30% | 0.00% | 80.56% | 5.16% | NA |
| Japonica Intermediate | 241 | 39.80% | 0.00% | 53.53% | 6.64% | NA |
| VI/Aromatic | 96 | 7.30% | 0.00% | 51.04% | 41.67% | NA |
| Intermediate | 90 | 33.30% | 0.00% | 57.78% | 8.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0401439086 | G -> DEL | LOC_Os04g03350.1 | N | frameshift_variant | Average:16.053; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg0401439086 | G -> A | LOC_Os04g03350.1 | missense_variant ; p.Ala127Thr; MODERATE | nonsynonymous_codon ; A127T | Average:16.053; most accessible tissue: Minghui63 panicle, score: 20.733 | benign  |
0.383 |
DELETERIOUS | 0.03 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0401439086 | 4.42E-06 | NA | mr1128_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 |