Search for Variation information by Variation ID:
Detailed information for vg0723665620:
| Variant ID: vg0723665620 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 23665620 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, G: 0.04, others allele: 0.00, population size: 268. )
Flanking Sequence (100 bp) in Reference Genome:
AACTTTTTTGTGTACTAGGTTGTAGATGTGGAAAGTGTTGACAACACAGATGTGGCTGCTGTGACTGTTGAAATTGATGAACAATTGGATGAAGATGCAT[C/G]
TGAAAATGATGAAGAAGAAAAGGATGTTGTTTATTCCCCACCAATTGTTCCATACATTGGAATGGAGTTTGATACAGTGGAAGAGGCAAGAAATGTTTAC
Reverse complement sequence
GTAAACATTTCTTGCCTCTTCCACTGTATCAAACTCCATTCCAATGTATGGAACAATTGGTGGGGAATAAACAACATCCTTTTCTTCTTCATCATTTTCA[G/C]
ATGCATCTTCATCCAATTGTTCATCAATTTCAACAGTCACAGCAGCCACATCTGTGTTGTCAACACTTTCCACATCTACAACCTAGTACACAAAAAAGTT
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 86.60% | 11.80% | 0.51% | 1.12% | NA |
| All Indica | 2759 | 92.10% | 5.70% | 0.51% | 1.78% | NA |
| All Japonica | 1512 | 78.20% | 21.30% | 0.46% | 0.07% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 96.30% | 2.80% | 0.43% | 0.43% | NA |
| Indica III | 913 | 86.60% | 8.10% | 0.77% | 4.49% | NA |
| Indica Intermediate | 786 | 90.70% | 7.90% | 0.64% | 0.76% | NA |
| Temperate Japonica | 767 | 90.10% | 9.00% | 0.78% | 0.13% | NA |
| Tropical Japonica | 504 | 70.60% | 29.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 56.00% | 43.60% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 28.10% | 67.70% | 2.08% | 2.08% | NA |
| Intermediate | 90 | 84.40% | 13.30% | 1.11% | 1.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0723665620 | C -> DEL | LOC_Os07g39490.1 | N | frameshift_variant | Average:33.185; most accessible tissue: Zhenshan97 flag leaf, score: 51.466 | N | N | N | N |
| vg0723665620 | C -> G | LOC_Os07g39490.1 | missense_variant ; p.Ser87Cys; MODERATE | nonsynonymous_codon ; S87C | Average:33.185; most accessible tissue: Zhenshan97 flag leaf, score: 51.466 | probably damaging  |
2.8 |
TOLERATED | 0.06 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0723665620 | 4.75E-06 | 7.53E-08 | Grain_thickness | Ind_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 |
| vg0723665620 | 7.74E-06 | 2.80E-06 | Grain_weight | Ind_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 |