Search for Variation information by Variation ID:
Detailed information for vg0403728255:
| Variant ID: vg0403728255 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 3728255 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 186. )
Flanking Sequence (100 bp) in Reference Genome:
TAGACCTCTCGGTACGATTTCACTTCGGCATGCTTTGCTCATGAAAATGATACGGAATACTGAAAGAACACTTTGCAGGAAACCATCTGACATAGATCCA[A/T]
CTGGAAAAGATCCTGATCCAGCCGCGACAGAAGCAAACGTATCCAAGGATCCTGAGACGACTGCCGAAAGCCAGCCGACTGCCGAAAGCCAGCCGACTGG
Reverse complement sequence
CCAGTCGGCTGGCTTTCGGCAGTCGGCTGGCTTTCGGCAGTCGTCTCAGGATCCTTGGATACGTTTGCTTCTGTCGCGGCTGGATCAGGATCTTTTCCAG[T/A]
TGGATCTATGTCAGATGGTTTCCTGCAAAGTGTTCTTTCAGTATTCCGTATCATTTTCATGAGCAAAGCATGCCGAAGTGAAATCGTACCGAGAGGTCTA
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 92.10% | 0.50% | 4.00% | 3.43% | NA |
| All Indica | 2759 | 87.00% | 0.70% | 6.56% | 5.73% | NA |
| All Japonica | 1512 | 99.80% | 0.10% | 0.07% | 0.07% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.00% | 0.37% | NA |
| Indica I | 595 | 80.20% | 1.20% | 8.91% | 9.75% | NA |
| Indica II | 465 | 85.80% | 0.60% | 10.54% | 3.01% | NA |
| Indica III | 913 | 89.00% | 0.20% | 3.94% | 6.79% | NA |
| Indica Intermediate | 786 | 90.60% | 0.90% | 5.47% | 3.05% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.20% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 91.70% | 2.10% | 6.25% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 0.00% | 1.11% | 2.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0403728255 | A -> DEL | LOC_Os04g07030.1 | N | frameshift_variant | Average:48.817; most accessible tissue: Minghui63 young leaf, score: 59.171 | N | N | N | N |
| vg0403728255 | A -> T | LOC_Os04g07030.1 | missense_variant ; p.Thr399Ser; MODERATE | nonsynonymous_codon ; T399S | Average:48.817; most accessible tissue: Minghui63 young leaf, score: 59.171 | benign  |
0.02 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0403728255 | 1.85E-06 | 1.85E-06 | mr1416_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 |