Search for Variation information by Variation ID:
Detailed information for vg1212722797:
| Variant ID: vg1212722797 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 12722797 |
| Reference Allele: G | Alternative Allele: A,T |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 286. )
Flanking Sequence (100 bp) in Reference Genome:
GACTGATAAGCGGTGAGAAGTCCGTGGGGGTCGCTGGGGAGTCCATGCCTCTGGTTATATTTATAGAGGGGGTGATTATGATCCAGGAATGGTGCACTAT[G/A,T]
GTGAGTTGTGTTGTGCAGGGGGTACTGTCACAGCCTCTATTCGGGTACTTTCCAGTATCGCGACGCATGGTAGACATGATGTTGAGGCTGTGTCTTGTGT
Reverse complement sequence
ACACAAGACACAGCCTCAACATCATGTCTACCATGCGTCGCGATACTGGAAAGTACCCGAATAGAGGCTGTGACAGTACCCCCTGCACAACACAACTCAC[C/T,A]
ATAGTGCACCATTCCTGGATCATAATCACCCCCTCTATAAATATAACCAGAGGCATGGACTCCCCAGCGACCCCCACGGACTTCTCACCGCTTATCAGTC
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 89.80% | 10.20% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 82.90% | 17.00% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 54.30% | 45.50% | 0.17% | 0.00% | NA |
| Indica II | 465 | 94.60% | 5.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 93.00% | 7.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 86.00% | 14.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 6.70% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1212722797 | G -> A | LOC_Os12g22540.1 | missense_variant&splice_region_variant ; p.Met52Ile; MODERATE | nonsynonymous_codon ; M52I | Average:59.045; most accessible tissue: Minghui63 young leaf, score: 79.896 | benign  |
0.281 |
TOLERATED | 0.28 |
| vg1212722797 | G -> T | LOC_Os12g22540.1 | missense_variant&splice_region_variant ; p.Met52Ile; MODERATE | N | Average:59.045; most accessible tissue: Minghui63 young leaf, score: 79.896 | N | N | N | N |
| vg1212722797 | G -> T | LOC_Os12g22530.1 | downstream_gene_variant ; 4343.0bp to feature; MODIFIER | N | Average:59.045; most accessible tissue: Minghui63 young leaf, score: 79.896 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1212722797 | NA | 5.41E-06 | mr1164_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 |
| vg1212722797 | NA | 1.26E-06 | mr1308_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 |
| vg1212722797 | NA | 1.02E-06 | mr1361_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 |
| vg1212722797 | NA | 7.84E-06 | mr1745_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 |