Search for Variation information by Variation ID:
Detailed information for vg0402121041:
| Variant ID: vg0402121041 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 2121041 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ACAGATTGTTGCCATTCTTGCGTTTGTGCTATATTTTCCATGAGGTTGTACTGGATCTCTCCTGTCTGCATATCAAGGGTGTCCATTCTCCTAGTGATTT[C/T]
ACCCAAGTCCCAATGAGAGGAACTCGAGCGCCATTTACTTGGAGATGGAGGCACACCACTTGATCTGGAAGGTTGGTTGTCCCCCCCCAATGTATGTCAT
Reverse complement sequence
ATGACATACATTGGGGGGGGACAACCAACCTTCCAGATCAAGTGGTGTGCCTCCATCTCCAAGTAAATGGCGCTCGAGTTCCTCTCATTGGGACTTGGGT[G/A]
AAATCACTAGGAGAATGGACACCCTTGATATGCAGACAGGAGAGATCCAGTACAACCTCATGGAAAATATAGCACAAACGCAAGAATGGCAACAATCTGT
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 27.70% | 5.80% | 7.55% | 58.99% | NA |
| All Indica | 2759 | 24.60% | 0.50% | 10.69% | 64.19% | NA |
| All Japonica | 1512 | 38.50% | 15.80% | 0.66% | 45.04% | NA |
| Aus | 269 | 10.00% | 0.00% | 11.90% | 78.07% | NA |
| Indica I | 595 | 24.40% | 0.00% | 15.13% | 60.50% | NA |
| Indica II | 465 | 19.40% | 0.00% | 12.47% | 68.17% | NA |
| Indica III | 913 | 26.10% | 0.90% | 7.34% | 65.72% | NA |
| Indica Intermediate | 786 | 26.20% | 0.80% | 10.18% | 62.85% | NA |
| Temperate Japonica | 767 | 68.40% | 19.20% | 0.26% | 12.13% | NA |
| Tropical Japonica | 504 | 3.80% | 14.10% | 0.99% | 81.15% | NA |
| Japonica Intermediate | 241 | 15.80% | 8.70% | 1.24% | 74.27% | NA |
| VI/Aromatic | 96 | 1.00% | 8.30% | 8.33% | 82.29% | NA |
| Intermediate | 90 | 22.20% | 12.20% | 13.33% | 52.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0402121041 | C -> DEL | LOC_Os04g04460.1 | N | frameshift_variant | Average:8.535; most accessible tissue: Callus, score: 31.61 | N | N | N | N |
| vg0402121041 | C -> T | LOC_Os04g04460.1 | missense_variant ; p.Glu72Lys; MODERATE | nonsynonymous_codon ; E72K | Average:8.535; most accessible tissue: Callus, score: 31.61 | benign  |
0.278 |
TOLERATED | 0.06 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0402121041 | 8.94E-08 | NA | mr1871_2 | 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 |