Search for Variation information by Variation ID:
Detailed information for vg0715495349:
| Variant ID: vg0715495349 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 15495349 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ATGATGCGGACATTGGGAGTTCATGATCTTGTCAAACGTGTTGACGCGCGAACGTTGTCGGGAAGAGTGAGTAGTGGTTGCAACAAGTTCCTCAGGCTTA[C/T]
GCTTGCGGTCCTTGTGGTTGTTACTTCCACCCCCTCCCGTAGCCGGCGTATCCTTTTTTTGCTTCCAATTGGAGCCCGACTGCTTTGATGCGATGACGGC
Reverse complement sequence
GCCGTCATCGCATCAAAGCAGTCGGGCTCCAATTGGAAGCAAAAAAAGGATACGCCGGCTACGGGAGGGGGTGGAAGTAACAACCACAAGGACCGCAAGC[G/A]
TAAGCCTGAGGAACTTGTTGCAACCACTACTCACTCTTCCCGACAACGTTCGCGCGTCAACACGTTTGACAAGATCATGAACTCCCAATGTCCGCATCAT
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 | 95.10% | 1.10% | 0.38% | 3.36% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 86.00% | 3.00% | 0.93% | 10.05% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 85.50% | 5.50% | 1.43% | 7.56% | NA |
| Tropical Japonica | 504 | 92.90% | 0.00% | 0.20% | 6.94% | NA |
| Japonica Intermediate | 241 | 73.40% | 1.20% | 0.83% | 24.48% | NA |
| VI/Aromatic | 96 | 85.40% | 5.20% | 4.17% | 5.21% | NA |
| Intermediate | 90 | 94.40% | 3.30% | 0.00% | 2.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0715495349 | C -> DEL | LOC_Os07g26810.1 | N | frameshift_variant | Average:34.298; most accessible tissue: Minghui63 flag leaf, score: 57.188 | N | N | N | N |
| vg0715495349 | C -> T | LOC_Os07g26810.1 | missense_variant ; p.Arg209His; MODERATE | nonsynonymous_codon ; R209H | Average:34.298; most accessible tissue: Minghui63 flag leaf, score: 57.188 | benign  |
0.427 |
DELETERIOUS | 0.03 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0715495349 | 4.23E-06 | 4.23E-06 | mr1004_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 |