Search for Variation information by Variation ID:
Detailed information for vg0814797975:
| Variant ID: vg0814797975 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 14797975 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 277. )
Flanking Sequence (100 bp) in Reference Genome:
CATTTCTTGTTGGCTAAGGACCATTTCGCATGCTCGAAGTCATACGACATTATGGTGGGAGCATTGTCCCTCTGTCTCTTTTGCCAGTAAGCATCTGACT[C/T]
ATTTTCACCTCTGACAAGTGCAGCAGGTTCTATAGGACATGGGGTAGTCAACACCCAGTCCACCTCTCCCAAGATAAAAGCAAGGTCGAGTTTTCTTTTC
Reverse complement sequence
GAAAAGAAAACTCGACCTTGCTTTTATCTTGGGAGAGGTGGACTGGGTGTTGACTACCCCATGTCCTATAGAACCTGCTGCACTTGTCAGAGGTGAAAAT[G/A]
AGTCAGATGCTTACTGGCAAAAGAGACAGAGGGACAATGCTCCCACCATAATGTCGTATGACTTCGAGCATGCGAAATGGTCCTTAGCCAACAAGAAATG
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 | 49.70% | 2.10% | 1.16% | 47.04% | NA |
| All Indica | 2759 | 17.00% | 3.50% | 1.96% | 77.53% | NA |
| All Japonica | 1512 | 98.40% | 0.00% | 0.07% | 1.52% | NA |
| Aus | 269 | 85.90% | 1.90% | 0.00% | 12.27% | NA |
| Indica I | 595 | 3.00% | 10.80% | 3.87% | 82.35% | NA |
| Indica II | 465 | 13.10% | 2.60% | 0.65% | 83.66% | NA |
| Indica III | 913 | 24.50% | 0.00% | 1.64% | 73.82% | NA |
| Indica Intermediate | 786 | 21.20% | 2.50% | 1.65% | 74.55% | NA |
| Temperate Japonica | 767 | 98.00% | 0.00% | 0.00% | 1.96% | NA |
| Tropical Japonica | 504 | 99.00% | 0.00% | 0.20% | 0.79% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.00% | 0.00% | 1.66% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 71.10% | 0.00% | 0.00% | 28.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0814797975 | C -> T | LOC_Os08g24500.1 | missense_variant ; p.Glu52Lys; MODERATE | nonsynonymous_codon ; E52K | Average:38.845; most accessible tissue: Zhenshan97 panicle, score: 52.263 | benign  |
0.278 |
DELETERIOUS | 0.03 |
| vg0814797975 | C -> DEL | LOC_Os08g24500.1 | N | frameshift_variant | Average:38.845; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0814797975 | 4.03E-07 | NA | mr1519 | 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 |
| vg0814797975 | 1.10E-07 | 7.85E-09 | mr1519 | 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 |
| vg0814797975 | 8.56E-07 | NA | mr1519_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 |
| vg0814797975 | 1.93E-06 | 1.51E-09 | mr1519_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 |