Search for Variation information by Variation ID:
Detailed information for vg0706176980:
| Variant ID: vg0706176980 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 6176980 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GCGTTAGCCAAATTTATGGTTGTCCCACACTACACCTACTTGATGATGAATATGCCAGGGCCTCGTGGAGTCATATCTTTGCGAAGCGACATCAAGAAAG[C/T]
TGTCACCTACGACAAGGAAAGCTGCGAGATGGCCCAGACTCATGAGATTACACTTGCCCATGAATCAATCCGACTGGCTGCATCAACTACGACCGAAGGA
Reverse complement sequence
TCCTTCGGTCGTAGTTGATGCAGCCAGTCGGATTGATTCATGGGCAAGTGTAATCTCATGAGTCTGGGCCATCTCGCAGCTTTCCTTGTCGTAGGTGACA[G/A]
CTTTCTTGATGTCGCTTCGCAAAGATATGACTCCACGAGGCCCTGGCATATTCATCATCAAGTAGGTGTAGTGTGGGACAACCATAAATTTGGCTAACGC
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 | 91.40% | 3.30% | 0.91% | 4.32% | NA |
| All Indica | 2759 | 97.00% | 0.10% | 0.25% | 2.65% | NA |
| All Japonica | 1512 | 89.00% | 9.90% | 1.12% | 0.00% | NA |
| Aus | 269 | 46.50% | 0.00% | 6.69% | 46.84% | NA |
| Indica I | 595 | 97.80% | 0.00% | 0.17% | 2.02% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 97.40% | 0.00% | 0.22% | 2.41% | NA |
| Indica Intermediate | 786 | 94.30% | 0.30% | 0.51% | 4.96% | NA |
| Temperate Japonica | 767 | 93.60% | 5.00% | 1.43% | 0.00% | NA |
| Tropical Japonica | 504 | 82.30% | 16.70% | 0.99% | 0.00% | NA |
| Japonica Intermediate | 241 | 88.40% | 11.20% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 86.70% | 7.80% | 1.11% | 4.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0706176980 | C -> DEL | LOC_Os07g11220.1 | N | frameshift_variant | Average:53.129; most accessible tissue: Zhenshan97 young leaf, score: 78.938 | N | N | N | N |
| vg0706176980 | C -> T | LOC_Os07g11220.1 | missense_variant ; p.Ala99Val; MODERATE | nonsynonymous_codon ; A99V | Average:53.129; most accessible tissue: Zhenshan97 young leaf, score: 78.938 | benign  |
1.453 |
DELETERIOUS | 0.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0706176980 | 4.90E-06 | 4.90E-06 | mr1669_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 |
| vg0706176980 | NA | 7.51E-06 | mr1861_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 |