Search for Variation information by Variation ID:
Detailed information for vg0608710017:
| Variant ID: vg0608710017 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 8710017 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.65, C: 0.36, others allele: 0.00, population size: 113. )
Flanking Sequence (100 bp) in Reference Genome:
CGTACGCGCCTTCCACCAACTCAATTTCGACCTTGGAGTATCCTGCTGGAATCGGCCTGCAGTGGTAAGTCCCTGAAGGGTCCGTTGGGATGGCCATGCC[T/C]
GACGCCACCTTCACGTGGTGATAGGTTATTTATTAGTAATCAACATATATAAGCAGCAACTTGCGGAATGGACAAGTCTAAAATCTATAAACTACGAGCT
Reverse complement sequence
AGCTCGTAGTTTATAGATTTTAGACTTGTCCATTCCGCAAGTTGCTGCTTATATATGTTGATTACTAATAAATAACCTATCACCACGTGAAGGTGGCGTC[A/G]
GGCATGGCCATCCCAACGGACCCTTCAGGGACTTACCACTGCAGGCCGATTCCAGCAGGATACTCCAAGGTCGAAATTGAGTTGGTGGAAGGCGCGTACG
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 | 43.50% | 25.50% | 25.67% | 5.37% | NA |
| All Indica | 2759 | 6.50% | 42.20% | 42.55% | 8.84% | NA |
| All Japonica | 1512 | 99.00% | 0.20% | 0.66% | 0.13% | NA |
| Aus | 269 | 86.20% | 10.80% | 2.97% | 0.00% | NA |
| Indica I | 595 | 2.00% | 48.20% | 38.82% | 10.92% | NA |
| Indica II | 465 | 5.40% | 23.20% | 57.20% | 14.19% | NA |
| Indica III | 913 | 7.30% | 57.40% | 32.09% | 3.18% | NA |
| Indica Intermediate | 786 | 9.40% | 31.00% | 48.85% | 10.69% | NA |
| Temperate Japonica | 767 | 99.10% | 0.00% | 0.65% | 0.26% | NA |
| Tropical Japonica | 504 | 99.20% | 0.40% | 0.40% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.40% | 1.24% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 57.80% | 10.00% | 23.33% | 8.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0608710017 | T -> C | LOC_Os06g15340.1 | synonymous_variant ; p.Ser303Ser; LOW | synonymous_codon | Average:11.719; most accessible tissue: Callus, score: 22.533 | N | N | N | N |
| vg0608710017 | T -> C | LOC_Os06g15340.1 | synonymous_variant ; p.Ser303Ser; LOW | nonsynonymous_codon ; S303L | Average:11.719; most accessible tissue: Callus, score: 22.533 | benign  |
1.097 |
DELETERIOUS | 0.01 |
| vg0608710017 | T -> DEL | LOC_Os06g15340.1 | N | frameshift_variant | Average:11.719; most accessible tissue: Callus, score: 22.533 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0608710017 | NA | 2.96E-30 | mr1204 | 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 |
| vg0608710017 | 3.44E-06 | 1.74E-07 | mr1241 | 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 |
| vg0608710017 | NA | 1.88E-06 | mr1748 | 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 |
| vg0608710017 | NA | 3.63E-32 | mr1878 | 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 |