Search for Variation information by Variation ID:
Detailed information for vg0712941986:
| Variant ID: vg0712941986 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 12941986 |
| Reference Allele: C | Alternative Allele: A,T |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TCACCTTGGTCTTCCTAGGGGCCTTAGAAGTCGAAGCTCCACTCTTATTTTCTTTCCAAACACCCACCTCCGGCTTCTTTGGCACTATCATCTTAGGCCT[C/A,T]
GGTTCACCAATGACCACTTCCTTTCCCTTAGTAGATTCGGCTTGCTCCGGCCGAATCAACACCTTCTTATCATTGAAATTAATTGTGTTCACCGGAAAAG
Reverse complement sequence
CTTTTCCGGTGAACACAATTAATTTCAATGATAAGAAGGTGTTGATTCGGCCGGAGCAAGCCGAATCTACTAAGGGAAAGGAAGTGGTCATTGGTGAACC[G/T,A]
AGGCCTAAGATGATAGTGCCAAAGAAGCCGGAGGTGGGTGTTTGGAAAGAAAATAAGAGTGGAGCTTCGACTTCTAAGGCCCCTAGGAAGACCAAGGTGA
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 | 47.90% | 1.40% | 28.04% | 22.26% | T: 0.40% |
| All Indica | 2759 | 23.10% | 2.00% | 42.23% | 32.22% | T: 0.47% |
| All Japonica | 1512 | 87.70% | 0.10% | 4.76% | 7.41% | NA |
| Aus | 269 | 72.50% | 0.00% | 16.73% | 9.67% | T: 1.12% |
| Indica I | 595 | 23.90% | 5.70% | 25.04% | 45.21% | T: 0.17% |
| Indica II | 465 | 30.10% | 0.90% | 37.63% | 31.18% | T: 0.22% |
| Indica III | 913 | 15.90% | 0.30% | 56.19% | 26.83% | T: 0.77% |
| Indica Intermediate | 786 | 26.80% | 1.70% | 41.73% | 29.26% | T: 0.51% |
| Temperate Japonica | 767 | 85.30% | 0.00% | 4.82% | 9.91% | NA |
| Tropical Japonica | 504 | 92.90% | 0.40% | 3.97% | 2.78% | NA |
| Japonica Intermediate | 241 | 84.60% | 0.00% | 6.22% | 9.13% | NA |
| VI/Aromatic | 96 | 55.20% | 7.30% | 25.00% | 9.38% | T: 3.12% |
| Intermediate | 90 | 60.00% | 1.10% | 21.11% | 17.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0712941986 | C -> DEL | LOC_Os07g22960.1 | N | frameshift_variant | Average:14.159; most accessible tissue: Callus, score: 25.837 | N | N | N | N |
| vg0712941986 | C -> A | LOC_Os07g22960.1 | synonymous_variant ; p.Pro859Pro; LOW | synonymous_codon | Average:14.159; most accessible tissue: Callus, score: 25.837 | N | N | N | N |
| vg0712941986 | C -> T | LOC_Os07g22960.1 | synonymous_variant ; p.Pro859Pro; LOW | synonymous_codon | Average:14.159; most accessible tissue: Callus, score: 25.837 | N | N | N | N |
| vg0712941986 | C -> T | LOC_Os07g22960.1 | synonymous_variant ; p.Pro859Pro; LOW | nonsynonymous_codon ; P859L | Average:14.159; most accessible tissue: Callus, score: 25.837 | benign  |
0.289 |
DELETERIOUS | 0.02 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0712941986 | NA | 6.49E-08 | Awn_length | Jap_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 |
| vg0712941986 | 1.15E-06 | 1.15E-06 | mr1067 | 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 |
| vg0712941986 | NA | 6.30E-07 | mr1080 | 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 |
| vg0712941986 | NA | 3.23E-07 | mr1962 | 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 |