Search for Variation information by Variation ID:
Detailed information for vg0403205829:
| Variant ID: vg0403205829 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 3205829 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.88, T: 0.12, others allele: 0.00, population size: 57. )
Flanking Sequence (100 bp) in Reference Genome:
AGTACTGTTGCAGGGATTGAGTTAACAGGGAACGTACGCAGTACGACCTCCGGTGCTGCTTGTGCCTCCTCTGCAGACGCGTGGTTGACACGAGCCTGGA[T/C]
AAACCTTGGCCCGGCACGCCTAGGCTTCGGGCATTTGTCGGCGAAATGGCCAAGCTCGCCACAGTTGAAACAGGACCCTGGTTTTGCTCCAGTCTCCTTC
Reverse complement sequence
GAAGGAGACTGGAGCAAAACCAGGGTCCTGTTTCAACTGTGGCGAGCTTGGCCATTTCGCCGACAAATGCCCGAAGCCTAGGCGTGCCGGGCCAAGGTTT[A/G]
TCCAGGCTCGTGTCAACCACGCGTCTGCAGAGGAGGCACAAGCAGCACCGGAGGTCGTACTGCGTACGTTCCCTGTTAACTCAATCCCTGCAACAGTACT
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 73.10% | 0.10% | 2.84% | 23.97% | NA |
| All Indica | 2759 | 73.10% | 0.10% | 2.72% | 24.03% | NA |
| All Japonica | 1512 | 69.00% | 0.00% | 2.65% | 28.31% | NA |
| Aus | 269 | 94.40% | 0.70% | 3.72% | 1.12% | NA |
| Indica I | 595 | 67.10% | 0.00% | 1.68% | 31.26% | NA |
| Indica II | 465 | 73.50% | 0.00% | 3.01% | 23.44% | NA |
| Indica III | 913 | 77.00% | 0.20% | 2.74% | 20.04% | NA |
| Indica Intermediate | 786 | 73.00% | 0.10% | 3.31% | 23.54% | NA |
| Temperate Japonica | 767 | 86.80% | 0.00% | 1.43% | 11.73% | NA |
| Tropical Japonica | 504 | 45.60% | 0.00% | 4.56% | 49.80% | NA |
| Japonica Intermediate | 241 | 61.40% | 0.00% | 2.49% | 36.10% | NA |
| VI/Aromatic | 96 | 79.20% | 0.00% | 2.08% | 18.75% | NA |
| Intermediate | 90 | 68.90% | 0.00% | 7.78% | 23.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0403205829 | T -> C | LOC_Os04g06144.1 | missense_variant ; p.Ile85Val; MODERATE | nonsynonymous_codon ; I85V | Average:32.382; most accessible tissue: Minghui63 young leaf, score: 51.901 | benign  |
-0.361 |
TOLERATED | 0.49 |
| vg0403205829 | T -> DEL | LOC_Os04g06144.1 | N | frameshift_variant | Average:32.382; most accessible tissue: Minghui63 young leaf, score: 51.901 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0403205829 | 4.46E-07 | NA | mr1410 | 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 |
| vg0403205829 | 9.33E-08 | NA | mr1301_2 | 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 |
| vg0403205829 | 9.73E-08 | NA | mr1410_2 | 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 |