Search for Variation information by Variation ID:
Detailed information for vg0706563568:
| Variant ID: vg0706563568 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 6563568 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AAGTCTTTCCTGATGTCAGCAAGAACTAAAATAGGCGCAGAGGTCAACTTTTCTTTGAGCTGCTCAAAGCTTTCCTGACACTGTTCTGACCACACAAACT[T/C]
CTTTTCCTTCTTGAGTAGTTGTGTCATTGGTCGGGCTATCTTAGAGAATCCTTGAATGAACCTTCGGTAGTATCCGGCCAAACCTAGAAAACTCCGAATC
Reverse complement sequence
GATTCGGAGTTTTCTAGGTTTGGCCGGATACTACCGAAGGTTCATTCAAGGATTCTCTAAGATAGCCCGACCAATGACACAACTACTCAAGAAGGAAAAG[A/G]
AGTTTGTGTGGTCAGAACAGTGTCAGGAAAGCTTTGAGCAGCTCAAAGAAAAGTTGACCTCTGCGCCTATTTTAGTTCTTGCTGACATCAGGAAAGACTT
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 89.50% | 4.70% | 5.78% | 0.04% | NA |
| All Indica | 2759 | 83.40% | 7.20% | 9.28% | 0.07% | NA |
| All Japonica | 1512 | 99.60% | 0.00% | 0.40% | 0.00% | NA |
| Aus | 269 | 94.10% | 4.10% | 1.86% | 0.00% | NA |
| Indica I | 595 | 89.20% | 3.20% | 7.56% | 0.00% | NA |
| Indica II | 465 | 72.70% | 13.10% | 14.19% | 0.00% | NA |
| Indica III | 913 | 85.80% | 6.60% | 7.56% | 0.11% | NA |
| Indica Intermediate | 786 | 82.60% | 7.60% | 9.67% | 0.13% | NA |
| Temperate Japonica | 767 | 99.50% | 0.00% | 0.52% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 84.40% | 10.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0706563568 | T -> DEL | LOC_Os07g11860.1 | N | frameshift_variant | Average:8.934; most accessible tissue: Callus, score: 18.471 | N | N | N | N |
| vg0706563568 | T -> C | LOC_Os07g11860.1 | missense_variant ; p.Lys961Glu; MODERATE | nonsynonymous_codon ; K961E | Average:8.934; most accessible tissue: Callus, score: 18.471 | benign  |
0.802 |
DELETERIOUS | 0.01 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0706563568 | 1.14E-06 | 8.38E-07 | mr1742 | Ind_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 |