Search for Variation information by Variation ID:
Detailed information for vg0401412219:
| Variant ID: vg0401412219 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 1412219 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AATATGAAAAATTATCAACTTAATTGTAATCAACGAATTGCAGATCAAGTTGTCGGCGGATGAACAGGTGACTTCGGTGGAGGGCACCATCGGGCGTTTC[A/T]
GGGACGTGGATGAGCCTGTGATTACCTCCCTAACATTCCGGACCAACGCCGGCAAGACATACGGACCATACGGCGGCGCCAGCGACAAGCAAGCTGGCAC
Reverse complement sequence
GTGCCAGCTTGCTTGTCGCTGGCGCCGCCGTATGGTCCGTATGTCTTGCCGGCGTTGGTCCGGAATGTTAGGGAGGTAATCACAGGCTCATCCACGTCCC[T/A]
GAAACGCCCGATGGTGCCCTCCACCGAAGTCACCTGTTCATCCGCCGACAACTTGATCTGCAATTCGTTGATTACAATTAAGTTGATAATTTTTCATATT
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 | 92.90% | 4.50% | 0.44% | 2.16% | NA |
| All Indica | 2759 | 92.30% | 7.60% | 0.04% | 0.04% | NA |
| All Japonica | 1512 | 92.30% | 0.10% | 1.12% | 6.48% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 92.40% | 7.40% | 0.00% | 0.17% | NA |
| Indica II | 465 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Indica III | 913 | 87.30% | 12.70% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 94.10% | 5.70% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 93.90% | 0.00% | 1.83% | 4.30% | NA |
| Tropical Japonica | 504 | 88.10% | 0.20% | 0.40% | 11.31% | NA |
| Japonica Intermediate | 241 | 95.90% | 0.40% | 0.41% | 3.32% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 1.04% | 3.12% | NA |
| Intermediate | 90 | 95.60% | 2.20% | 2.22% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0401412219 | A -> DEL | LOC_Os04g03320.1 | N | frameshift_variant | Average:56.72; most accessible tissue: Zhenshan97 panicle, score: 75.67 | N | N | N | N |
| vg0401412219 | A -> T | LOC_Os04g03320.1 | missense_variant ; p.Arg117Trp; MODERATE | nonsynonymous_codon ; R117W | Average:56.72; most accessible tissue: Zhenshan97 panicle, score: 75.67 | probably damaging  |
3.422 |
TOLERATED | 0.12 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0401412219 | 3.22E-07 | NA | mr1141 | 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 |
| vg0401412219 | NA | 8.28E-07 | mr1038_2 | 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 |
| vg0401412219 | NA | 1.77E-06 | mr1389_2 | 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 |