Search for Variation information by Variation ID:
Detailed information for vg0713522995:
| Variant ID: vg0713522995 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 13522995 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ATAAATTCAAAATTTCATTGCGTACGTATCAATTTGTTGTTTACTAATTAATTTCATACATTCATAGGTTATTCGCATGAGGGATAACCTCACACACAAG[A/G]
AATTTATCGCGGCGGTTCAAGAACAACTCATGGAATTCATCAACGAACAAATCCTTGATCTTGAGGGTGAATTCTACTACGACGGAAATACAATTCATAG
Reverse complement sequence
CTATGAATTGTATTTCCGTCGTAGTAGAATTCACCCTCAAGATCAAGGATTTGTTCGTTGATGAATTCCATGAGTTGTTCTTGAACCGCCGCGATAAATT[T/C]
CTTGTGTGTGAGGTTATCCCTCATGCGAATAACCTATGAATGTATGAAATTAATTAGTAAACAACAAATTGATACGTACGCAATGAAATTTTGAATTTAT
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 | 84.20% | 8.00% | 1.04% | 6.73% | NA |
| All Indica | 2759 | 88.30% | 1.00% | 0.91% | 9.82% | NA |
| All Japonica | 1512 | 76.50% | 22.10% | 1.46% | 0.00% | NA |
| Aus | 269 | 82.20% | 1.90% | 0.74% | 15.24% | NA |
| Indica I | 595 | 69.20% | 1.00% | 1.85% | 27.90% | NA |
| Indica II | 465 | 92.90% | 1.70% | 1.08% | 4.30% | NA |
| Indica III | 913 | 99.50% | 0.30% | 0.00% | 0.22% | NA |
| Indica Intermediate | 786 | 87.00% | 1.30% | 1.15% | 10.56% | NA |
| Temperate Japonica | 767 | 65.70% | 31.60% | 2.74% | 0.00% | NA |
| Tropical Japonica | 504 | 90.10% | 9.90% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 82.20% | 17.40% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 78.90% | 14.40% | 0.00% | 6.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0713522995 | A -> DEL | LOC_Os07g23920.1 | N | frameshift_variant | Average:28.591; most accessible tissue: Zhenshan97 panicle, score: 36.038 | N | N | N | N |
| vg0713522995 | A -> G | LOC_Os07g23920.1 | missense_variant ; p.Lys734Glu; MODERATE | nonsynonymous_codon ; K734E | Average:28.591; most accessible tissue: Zhenshan97 panicle, score: 36.038 | benign  |
-0.278 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0713522995 | 7.92E-07 | 8.46E-08 | mr1955 | 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 |