Search for Variation information by Variation ID:
Detailed information for vg0906525063:
| Variant ID: vg0906525063 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 6525063 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 112. )
Flanking Sequence (100 bp) in Reference Genome:
TCATCAATGGGGCAGGTGGTTTCGTCCTGAGTTTGCATGGCGTCCATGCTCTGTGATCCTACCTGCCCCGTTGAGGCACAGCTACTACGATTGCCTGAGG[G/T]
GCTGACCATGATAGGAGGAATGTATGGCTGGGGATCCTGGCTCCGATATGCGGCCATGCGTTCATCCACCTTTCTTGCCACCTCCTCTTGCATGCTAAGC
Reverse complement sequence
GCTTAGCATGCAAGAGGAGGTGGCAAGAAAGGTGGATGAACGCATGGCCGCATATCGGAGCCAGGATCCCCAGCCATACATTCCTCCTATCATGGTCAGC[C/A]
CCTCAGGCAATCGTAGTAGCTGTGCCTCAACGGGGCAGGTAGGATCACAGAGCATGGACGCCATGCAAACTCAGGACGAAACCACCTGCCCCATTGATGA
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 51.90% | 22.40% | 6.77% | 18.94% | NA |
| All Indica | 2759 | 25.00% | 32.00% | 11.05% | 31.90% | NA |
| All Japonica | 1512 | 98.70% | 0.50% | 0.40% | 0.40% | NA |
| Aus | 269 | 60.20% | 39.00% | 0.74% | 0.00% | NA |
| Indica I | 595 | 31.80% | 4.40% | 10.59% | 53.28% | NA |
| Indica II | 465 | 17.80% | 54.00% | 8.17% | 20.00% | NA |
| Indica III | 913 | 20.80% | 36.60% | 15.12% | 27.49% | NA |
| Indica Intermediate | 786 | 29.00% | 34.70% | 8.40% | 27.86% | NA |
| Temperate Japonica | 767 | 99.30% | 0.40% | 0.00% | 0.26% | NA |
| Tropical Japonica | 504 | 97.60% | 0.40% | 1.19% | 0.79% | NA |
| Japonica Intermediate | 241 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 56.20% | 42.70% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 60.00% | 23.30% | 6.67% | 10.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0906525063 | G -> DEL | LOC_Os09g11690.1 | N | frameshift_variant | Average:40.52; most accessible tissue: Minghui63 young leaf, score: 80.562 | N | N | N | N |
| vg0906525063 | G -> T | LOC_Os09g11690.1 | missense_variant ; p.Pro170Thr; MODERATE | nonsynonymous_codon ; P170T | Average:40.52; most accessible tissue: Minghui63 young leaf, score: 80.562 | possibly damaging  |
1.867 |
DELETERIOUS | 0.01 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0906525063 | NA | 5.50E-06 | mr1036_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 |
| vg0906525063 | NA | 1.98E-07 | mr1169_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 |
| vg0906525063 | NA | 5.92E-06 | mr1169_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 |
| vg0906525063 | NA | 7.00E-07 | mr1842_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 |
| vg0906525063 | 5.67E-07 | 5.66E-07 | mr1947_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 |