Search for Variation information by Variation ID:
Detailed information for vg0432213299:
| Variant ID: vg0432213299 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 32213299 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AGACACGCTGCCAGATATCGACTTTAGGGATAGGCATGGCTATTCCCCTACGGTATCTCCGGATACCGTCAGGAGATACGAAAGCGCTATCTCTGATCTC[G/A]
CCGGGCACGGATTCGAGGAGGAAGACTACCCTGTTGTTGACTACGAGTCAGACTTTCAGACCAACATGTTGATAACAGTTAGATAGGCTGCCCACATATT
Reverse complement sequence
AATATGTGGGCAGCCTATCTAACTGTTATCAACATGTTGGTCTGAAAGTCTGACTCGTAGTCAACAACAGGGTAGTCTTCCTCCTCGAATCCGTGCCCGG[C/T]
GAGATCAGAGATAGCGCTTTCGTATCTCCTGACGGTATCCGGAGATACCGTAGGGGAATAGCCATGCCTATCCCTAAAGTCGATATCTGGCAGCGTGTCT
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 | 90.10% | 9.90% | 0.00% | 0.02% | NA |
| All Indica | 2759 | 93.80% | 6.20% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 81.50% | 18.50% | 0.00% | 0.07% | NA |
| Aus | 269 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Indica II | 465 | 89.90% | 10.10% | 0.00% | 0.00% | NA |
| Indica III | 913 | 95.00% | 5.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 90.80% | 9.20% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 51.00% | 48.80% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 93.40% | 6.60% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 83.30% | 16.70% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0432213299 | G -> DEL | LOC_Os04g54050.1 | N | frameshift_variant | Average:18.829; most accessible tissue: Minghui63 panicle, score: 29.741 | N | N | N | N |
| vg0432213299 | G -> A | LOC_Os04g54050.1 | missense_variant ; p.Ala429Thr; MODERATE | nonsynonymous_codon ; A429I | Average:18.829; most accessible tissue: Minghui63 panicle, score: 29.741 | possibly damaging  |
1.8 |
DELETERIOUS | 0.02 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0432213299 | 3.75E-06 | 1.40E-08 | mr1657 | Jap_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 |
| vg0432213299 | 8.58E-07 | NA | mr1817 | Jap_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 |
| vg0432213299 | NA | 3.31E-07 | mr1890 | Jap_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 |
| vg0432213299 | NA | 1.93E-06 | mr1277_2 | Jap_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 |