Search for Variation information by Variation ID:
Detailed information for vg0408377327:
| Variant ID: vg0408377327 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 8377327 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 123. )
Flanking Sequence (100 bp) in Reference Genome:
CATAGCGAGCTAAGAGATTAAAGTCATGGAGGTACTCTATGACAGAACGGGATCCCTGATTGAGTGCTCTGAACTCTCTCTTCTTCAGGGCCACAACTCC[T/C]
GATGGAATATGTGTCTTCTTGAAAGCAGCAGTAAACTCCCGCCAAGTGATAAGCTCTCCCACAGCTCTGTTTTGGCGAAAATGATCCCACCACTCAGCAG
Reverse complement sequence
CTGCTGAGTGGTGGGATCATTTTCGCCAAAACAGAGCTGTGGGAGAGCTTATCACTTGGCGGGAGTTTACTGCTGCTTTCAAGAAGACACATATTCCATC[A/G]
GGAGTTGTGGCCCTGAAGAAGAGAGAGTTCAGAGCACTCAATCAGGGATCCCGTTCTGTCATAGAGTACCTCCATGACTTTAATCTCTTAGCTCGCTATG
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 | 75.60% | 4.70% | 12.53% | 7.17% | NA |
| All Indica | 2759 | 76.60% | 6.40% | 17.00% | 0.00% | NA |
| All Japonica | 1512 | 73.70% | 0.30% | 3.84% | 22.09% | NA |
| Aus | 269 | 80.70% | 4.10% | 15.24% | 0.00% | NA |
| Indica I | 595 | 68.20% | 9.70% | 22.02% | 0.00% | NA |
| Indica II | 465 | 82.60% | 4.50% | 12.90% | 0.00% | NA |
| Indica III | 913 | 77.30% | 5.40% | 17.31% | 0.00% | NA |
| Indica Intermediate | 786 | 78.60% | 6.10% | 15.27% | 0.00% | NA |
| Temperate Japonica | 767 | 96.60% | 0.00% | 0.13% | 3.26% | NA |
| Tropical Japonica | 504 | 37.10% | 0.60% | 10.91% | 51.39% | NA |
| Japonica Intermediate | 241 | 77.60% | 0.80% | 0.83% | 20.75% | NA |
| VI/Aromatic | 96 | 57.30% | 22.90% | 15.62% | 4.17% | NA |
| Intermediate | 90 | 78.90% | 10.00% | 10.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0408377327 | T -> C | LOC_Os04g14890.1 | synonymous_variant ; p.Ser305Ser; LOW | synonymous_codon | Average:36.927; most accessible tissue: Zhenshan97 flag leaf, score: 58.104 | N | N | N | N |
| vg0408377327 | T -> C | LOC_Os04g14890.1 | synonymous_variant ; p.Ser305Ser; LOW | nonsynonymous_codon ; S305P | Average:36.927; most accessible tissue: Zhenshan97 flag leaf, score: 58.104 | probably damaging  |
2.057 |
DELETERIOUS | 0.00 |
| vg0408377327 | T -> DEL | LOC_Os04g14890.1 | N | frameshift_variant | Average:36.927; most accessible tissue: Zhenshan97 flag leaf, score: 58.104 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0408377327 | 7.60E-06 | 8.13E-06 | mr1350_2 | 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 |