Search for Variation information by Variation ID:
Detailed information for vg0509203069:
| Variant ID: vg0509203069 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 9203069 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.79, T: 0.21, others allele: 0.00, population size: 227. )
Flanking Sequence (100 bp) in Reference Genome:
ACTAGCCAACCCTAACCTGGGTCACTGGAAGAATACCTTCAAGTCTTGGCCATCTCTTGAAAAACCTACTCCTGATAAGAGCTGGATCACCTGGTACCAA[T/C]
GCGTATCGGCTAGTAAGAAAGTTCACTGGGATAAGATTGGAATCGGCCAAGCGCTTGCTCTCACCATAGCCAATTCTGCTAAGGATGAACCTCTGATGAC
Reverse complement sequence
GTCATCAGAGGTTCATCCTTAGCAGAATTGGCTATGGTGAGAGCAAGCGCTTGGCCGATTCCAATCTTATCCCAGTGAACTTTCTTACTAGCCGATACGC[A/G]
TTGGTACCAGGTGATCCAGCTCTTATCAGGAGTAGGTTTTTCAAGAGATGGCCAAGACTTGAAGGTATTCTTCCAGTGACCCAGGTTAGGGTTGGCTAGT
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 | 78.60% | 21.20% | 0.17% | 0.11% | NA |
| All Indica | 2759 | 72.20% | 27.40% | 0.25% | 0.18% | NA |
| All Japonica | 1512 | 99.10% | 0.80% | 0.07% | 0.00% | NA |
| Aus | 269 | 20.80% | 79.20% | 0.00% | 0.00% | NA |
| Indica I | 595 | 89.70% | 10.30% | 0.00% | 0.00% | NA |
| Indica II | 465 | 68.20% | 30.50% | 0.86% | 0.43% | NA |
| Indica III | 913 | 56.20% | 43.50% | 0.11% | 0.22% | NA |
| Indica Intermediate | 786 | 79.80% | 19.80% | 0.25% | 0.13% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 98.00% | 2.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.40% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 80.00% | 20.00% | 0.00% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0509203069 | T -> DEL | LOC_Os05g16260.1 | N | frameshift_variant | Average:39.697; most accessible tissue: Minghui63 young leaf, score: 54.11 | N | N | N | N |
| vg0509203069 | T -> C | LOC_Os05g16260.1 | missense_variant ; p.Cys92Arg; MODERATE | nonsynonymous_codon ; C92R | Average:39.697; most accessible tissue: Minghui63 young leaf, score: 54.11 | benign  |
-0.478 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0509203069 | NA | 4.10E-10 | mr1039 | Ind_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 |
| vg0509203069 | NA | 5.41E-06 | mr1632 | Ind_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 |
| vg0509203069 | NA | 4.13E-09 | mr1039_2 | Ind_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 |
| vg0509203069 | 1.17E-06 | NA | mr1514_2 | 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 |
| vg0509203069 | NA | 1.66E-06 | mr1514_2 | Ind_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 |
| vg0509203069 | 2.48E-06 | NA | mr1632_2 | 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 |
| vg0509203069 | NA | 1.36E-09 | mr1632_2 | Ind_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 |