Search for Variation information by Variation ID:
Detailed information for vg0617228589:
| Variant ID: vg0617228589 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 17228589 |
| 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: 295. )
Flanking Sequence (100 bp) in Reference Genome:
CGATAGCGTCAACCCTGGCATCAACCAAGTAGCCTCAACTTCAACGATGCTGGTGTGGACTCAAGTCAGCGAAATCGTTTTCCCGGTCTACACCACGATG[C/T]
CGATCTCGAATGGCCCAGCAATTACCAGGAGCAAGAACGGCGTGGTTACAACCCCGGTCGACTTCATGTCGAAAGATCCTCCTGCAGAAGCGGAGAACGG
Reverse complement sequence
CCGTTCTCCGCTTCTGCAGGAGGATCTTTCGACATGAAGTCGACCGGGGTTGTAACCACGCCGTTCTTGCTCCTGGTAATTGCTGGGCCATTCGAGATCG[G/A]
CATCGTGGTGTAGACCGGGAAAACGATTTCGCTGACTTGAGTCCACACCAGCATCGTTGAAGTTGAGGCTACTTGGTTGATGCCAGGGTTGACGCTATCG
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 | 97.60% | 1.70% | 0.21% | 0.44% | NA |
| All Indica | 2759 | 99.60% | 0.20% | 0.07% | 0.07% | NA |
| All Japonica | 1512 | 93.50% | 4.70% | 0.53% | 1.26% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.70% | 0.00% | 0.17% | 0.17% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.20% | 0.50% | 0.13% | 0.13% | NA |
| Temperate Japonica | 767 | 97.10% | 0.00% | 0.39% | 2.48% | NA |
| Tropical Japonica | 504 | 85.90% | 13.30% | 0.79% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.90% | 1.70% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 4.40% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0617228589 | C -> T | LOC_Os06g29910.1 | missense_variant ; p.Pro82Ser; MODERATE | nonsynonymous_codon ; P82S | Average:67.869; most accessible tissue: Minghui63 flag leaf, score: 81.811 | possibly damaging  |
1.739 |
DELETERIOUS | 0.04 |
| vg0617228589 | C -> DEL | LOC_Os06g29910.1 | N | frameshift_variant | Average:67.869; most accessible tissue: Minghui63 flag leaf, score: 81.811 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0617228589 | NA | 2.19E-08 | mr1136 | 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 |
| vg0617228589 | NA | 8.18E-09 | mr1188 | 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 |
| vg0617228589 | NA | 4.82E-06 | mr1448 | 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 |
| vg0617228589 | NA | 9.21E-08 | mr1125_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 |
| vg0617228589 | 1.09E-06 | 6.19E-12 | mr1188_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 |