Search for Variation information by Variation ID:
Detailed information for vg0908416726:
| Variant ID: vg0908416726 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 8416726 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TAGAATTGGGGTTCAAATGGAGTAAAGAAAGGCCGTATAAGTTCAAAACCAAGAGAAGAAATTCAGAAGGCGGAGGGAGAAAACCGCAGAGAATGTAGTC[C/G]
TCGATCGCAACCATGCGACCTAGGACAGGCTGGGGTTCAGTACCTCCTGCTTCTCTCTCCATGGTCCCACGACCGGGAAGGGCGCCATCCTCCTGTAGCT
Reverse complement sequence
AGCTACAGGAGGATGGCGCCCTTCCCGGTCGTGGGACCATGGAGAGAGAAGCAGGAGGTACTGAACCCCAGCCTGTCCTAGGTCGCATGGTTGCGATCGA[G/C]
GACTACATTCTCTGCGGTTTTCTCCCTCCGCCTTCTGAATTTCTTCTCTTGGTTTTGAACTTATACGGCCTTTCTTTACTCCATTTGAACCCCAATTCTA
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 82.10% | 8.80% | 5.04% | 4.10% | NA |
| All Indica | 2759 | 84.10% | 11.60% | 4.24% | 0.07% | NA |
| All Japonica | 1512 | 77.20% | 4.20% | 6.28% | 12.30% | NA |
| Aus | 269 | 84.80% | 11.50% | 3.72% | 0.00% | NA |
| Indica I | 595 | 96.50% | 1.30% | 2.18% | 0.00% | NA |
| Indica II | 465 | 97.40% | 2.20% | 0.43% | 0.00% | NA |
| Indica III | 913 | 65.70% | 26.70% | 7.45% | 0.11% | NA |
| Indica Intermediate | 786 | 88.30% | 7.30% | 4.33% | 0.13% | NA |
| Temperate Japonica | 767 | 99.00% | 0.10% | 0.65% | 0.26% | NA |
| Tropical Japonica | 504 | 46.00% | 10.90% | 14.09% | 28.97% | NA |
| Japonica Intermediate | 241 | 73.40% | 2.90% | 7.88% | 15.77% | NA |
| VI/Aromatic | 96 | 81.20% | 1.00% | 11.46% | 6.25% | NA |
| Intermediate | 90 | 93.30% | 1.10% | 5.56% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0908416726 | C -> G | LOC_Os09g14230.1 | missense_variant ; p.Glu48Asp; MODERATE | nonsynonymous_codon ; E48D | Average:40.756; most accessible tissue: Minghui63 panicle, score: 77.956 | benign  |
1.376 |
DELETERIOUS | 0.05 |
| vg0908416726 | C -> DEL | LOC_Os09g14230.1 | N | frameshift_variant | Average:40.756; most accessible tissue: Minghui63 panicle, score: 77.956 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0908416726 | 6.57E-06 | 6.57E-06 | mr1344 | 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 |
| vg0908416726 | 3.94E-06 | 3.94E-06 | mr1439 | 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 |
| vg0908416726 | 3.09E-06 | 1.00E-07 | mr1607 | 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 |
| vg0908416726 | 1.77E-06 | 1.77E-06 | mr1647 | 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 |
| vg0908416726 | 3.17E-06 | 8.47E-08 | mr1695 | 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 |