Search for Variation information by Variation ID:
Detailed information for vg0719650559:
| Variant ID: vg0719650559 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 19650559 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TACAAGCTTCTGCACCTACTGCTACTACTGATCACAATGCCAACAAGGCCTCGGAGTTGGCACGCAGCTGCTCCTTCTCCAGCACAAACATCTTCAGCCG[C/A]
GGCAGCGACTTGCCGGCCGTGTTCGGCCGCGGGGCCGCCATGTTTGCCGGGGTCGGGGTCGGGGCCGGGCGCGGCGCGGGCAGCTTGACGTCCTTGACGG
Reverse complement sequence
CCGTCAAGGACGTCAAGCTGCCCGCGCCGCGCCCGGCCCCGACCCCGACCCCGGCAAACATGGCGGCCCCGCGGCCGAACACGGCCGGCAAGTCGCTGCC[G/T]
CGGCTGAAGATGTTTGTGCTGGAGAAGGAGCAGCTGCGTGCCAACTCCGAGGCCTTGTTGGCATTGTGATCAGTAGTAGCAGTAGGTGCAGAAGCTTGTA
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 84.40% | 6.60% | 0.95% | 8.06% | NA |
| All Indica | 2759 | 96.90% | 0.10% | 0.87% | 2.14% | NA |
| All Japonica | 1512 | 78.80% | 20.20% | 0.13% | 0.79% | NA |
| Aus | 269 | 9.30% | 0.00% | 5.58% | 85.13% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.00% | 0.17% | NA |
| Indica II | 465 | 93.10% | 0.00% | 3.23% | 3.66% | NA |
| Indica III | 913 | 98.80% | 0.00% | 0.00% | 1.20% | NA |
| Indica Intermediate | 786 | 94.80% | 0.30% | 1.15% | 3.82% | NA |
| Temperate Japonica | 767 | 59.80% | 39.20% | 0.26% | 0.65% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 95.40% | 1.70% | 0.00% | 2.90% | NA |
| VI/Aromatic | 96 | 20.80% | 0.00% | 2.08% | 77.08% | NA |
| Intermediate | 90 | 86.70% | 3.30% | 2.22% | 7.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0719650559 | C -> DEL | LOC_Os07g32850.1 | N | frameshift_variant | Average:43.104; most accessible tissue: Zhenshan97 root, score: 72.671 | N | N | N | N |
| vg0719650559 | C -> A | LOC_Os07g32850.1 | synonymous_variant ; p.Pro140Pro; LOW | nonsynonymous_codon ; P140H | Average:43.104; most accessible tissue: Zhenshan97 root, score: 72.671 | probably damaging  |
2.753 |
DELETERIOUS | 0.01 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0719650559 | 9.25E-06 | NA | Heading_date | All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg0719650559 | 4.43E-06 | NA | Plant_height | All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg0719650559 | 1.53E-07 | NA | Spikelet_length | All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg0719650559 | 1.20E-06 | NA | Spikelet_length | Jap_All | YES | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |