Search for Variation information by Variation ID:
Detailed information for vg0622512118:
| Variant ID: vg0622512118 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 22512118 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.08, others allele: 0.00, population size: 96. )
Flanking Sequence (100 bp) in Reference Genome:
GGTAGCAGTTGTGTCATCAACACGTGACAGTCATGAGACTTTAGGTTTGTGAACTTCTTCTCCTTCGTGCTTATTATTCGCTTTATATTCATGGAGTATC[T/C]
AGATGGTACCTTGATGCTCTCCAAGCATTGAAACATACTATCCTTCTCTGCCTTGCTAAGAGTGTAGCTGGCTGGACTCAAGTAATGGATGCCTTTCTCC
Reverse complement sequence
GGAGAAAGGCATCCATTACTTGAGTCCAGCCAGCTACACTCTTAGCAAGGCAGAGAAGGATAGTATGTTTCAATGCTTGGAGAGCATCAAGGTACCATCT[A/G]
GATACTCCATGAATATAAAGCGAATAATAAGCACGAAGGAGAAGAAGTTCACAAACCTAAAGTCTCATGACTGTCACGTGTTGATGACACAACTGCTACC
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 45.70% | 9.90% | 4.80% | 39.67% | NA |
| All Indica | 2759 | 35.00% | 1.90% | 3.44% | 59.66% | NA |
| All Japonica | 1512 | 70.20% | 25.90% | 0.99% | 2.91% | NA |
| Aus | 269 | 14.90% | 3.30% | 32.71% | 49.07% | NA |
| Indica I | 595 | 14.60% | 0.70% | 0.84% | 83.87% | NA |
| Indica II | 465 | 24.10% | 1.70% | 2.80% | 71.40% | NA |
| Indica III | 913 | 56.50% | 1.80% | 5.37% | 36.36% | NA |
| Indica Intermediate | 786 | 31.80% | 3.20% | 3.56% | 61.45% | NA |
| Temperate Japonica | 767 | 51.20% | 47.10% | 0.13% | 1.56% | NA |
| Tropical Japonica | 504 | 90.10% | 2.00% | 2.78% | 5.16% | NA |
| Japonica Intermediate | 241 | 88.80% | 8.70% | 0.00% | 2.49% | NA |
| VI/Aromatic | 96 | 47.90% | 1.00% | 27.08% | 23.96% | NA |
| Intermediate | 90 | 51.10% | 12.20% | 3.33% | 33.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0622512118 | T -> C | LOC_Os06g38070.1 | missense_variant ; p.Arg556Gly; MODERATE | nonsynonymous_codon ; R556G | Average:10.377; most accessible tissue: Minghui63 flag leaf, score: 17.021 | benign  |
-0.101 |
TOLERATED | 1.00 |
| vg0622512118 | T -> DEL | LOC_Os06g38070.1 | N | frameshift_variant | Average:10.377; most accessible tissue: Minghui63 flag leaf, score: 17.021 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0622512118 | NA | 3.09E-08 | mr1037 | 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 |
| vg0622512118 | NA | 1.32E-06 | mr1064 | 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 |
| vg0622512118 | NA | 7.94E-06 | mr1536 | 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 |
| vg0622512118 | 5.67E-07 | 5.67E-07 | mr1609_2 | Jap_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 |