Search for Variation information by Variation ID:
Detailed information for vg1004557601:
| Variant ID: vg1004557601 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 4557601 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, A: 0.09, others allele: 0.00, population size: 204. )
Flanking Sequence (100 bp) in Reference Genome:
GAAGCAGGGGATTATGTGTATCTCTGTGTCACTCCGCTCAGGGGAGTACACTGCTTCCAAACCAAAGAAAAGTTGGCACCACGCTTTGTGGGATCATACC[A/G]
GATTTTGGAACATAGAGGTGAAGTCGCTTACCAACTAGAGCTTCCCTCCAGCATGCTTGGCATCCATAATGTGTTCCACGTCTCTCAGTTGAAGAAATGT
Reverse complement sequence
ACATTTCTTCAACTGAGAGACGTGGAACACATTATGGATGCCAAGCATGCTGGAGGGAAGCTCTAGTTGGTAAGCGACTTCACCTCTATGTTCCAAAATC[T/C]
GGTATGATCCCACAAAGCGTGGTGCCAACTTTTCTTTGGTTTGGAAGCAGTGTACTCCCCTGAGCGGAGTGACACAGAGATACACATAATCCCCTGCTTC
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 | 49.20% | 33.20% | 0.51% | 17.10% | NA |
| All Indica | 2759 | 51.90% | 32.40% | 0.69% | 14.97% | NA |
| All Japonica | 1512 | 49.70% | 42.40% | 0.13% | 7.74% | NA |
| Aus | 269 | 7.10% | 1.90% | 0.37% | 90.71% | NA |
| Indica I | 595 | 41.50% | 19.00% | 1.18% | 38.32% | NA |
| Indica II | 465 | 61.10% | 28.20% | 1.08% | 9.68% | NA |
| Indica III | 913 | 59.80% | 35.30% | 0.22% | 4.71% | NA |
| Indica Intermediate | 786 | 45.20% | 41.90% | 0.64% | 12.34% | NA |
| Temperate Japonica | 767 | 32.50% | 67.30% | 0.13% | 0.13% | NA |
| Tropical Japonica | 504 | 73.20% | 5.00% | 0.00% | 21.83% | NA |
| Japonica Intermediate | 241 | 55.60% | 41.50% | 0.41% | 2.49% | NA |
| VI/Aromatic | 96 | 81.20% | 0.00% | 0.00% | 18.75% | NA |
| Intermediate | 90 | 50.00% | 30.00% | 2.22% | 17.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1004557601 | A -> G | LOC_Os10g08390.1 | missense_variant ; p.Gln794Arg; MODERATE | nonsynonymous_codon ; Q794R | Average:30.238; most accessible tissue: Minghui63 flag leaf, score: 57.188 | possibly damaging  |
-1.62 |
TOLERATED | 0.80 |
| vg1004557601 | A -> DEL | LOC_Os10g08390.1 | N | frameshift_variant | Average:30.238; most accessible tissue: Minghui63 flag leaf, score: 57.188 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1004557601 | 2.42E-06 | 2.42E-06 | mr1208 | 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 |
| vg1004557601 | NA | 1.32E-06 | mr1446 | 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 |
| vg1004557601 | NA | 7.25E-08 | mr1603 | 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 |
| vg1004557601 | NA | 2.72E-07 | mr1603 | 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 |
| vg1004557601 | NA | 1.20E-06 | mr1768 | 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 |