Search for Variation information by Variation ID:
Detailed information for vg1212722921:
| Variant ID: vg1212722921 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 12722921 |
| 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: 0.98, A: 0.01, T: 0.01, others allele: 0.00, population size: 241. )
Flanking Sequence (100 bp) in Reference Genome:
ACTGTCACAGCCTCTATTCGGGTACTTTCCAGTATCGCGACGCATGGTAGACATGATGTTGAGGCTGTGTCTTGTGTGTACAGTGGTACACCTCTGGCCA[G/A,T]
AGTAAAACTATTCGAATAGCCGTGCCCACGGTTATGGGCGGGTTGAGTAATGTTTTTCGTGATTAGTCTCACACCTCTCACAACAATTATTGATGCTATA
Reverse complement sequence
TATAGCATCAATAATTGTTGTGAGAGGTGTGAGACTAATCACGAAAAACATTACTCAACCCGCCCATAACCGTGGGCACGGCTATTCGAATAGTTTTACT[C/T,A]
TGGCCAGAGGTGTACCACTGTACACACAAGACACAGCCTCAACATCATGTCTACCATGCGTCGCGATACTGGAAAGTACCCGAATAGAGGCTGTGACAGT
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 | 75.60% | 24.30% | 0.08% | 0.00% | T: 0.02% |
| All Indica | 2759 | 61.30% | 38.60% | 0.14% | 0.00% | T: 0.04% |
| All Japonica | 1512 | 96.30% | 3.70% | 0.00% | 0.00% | NA |
| Aus | 269 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 61.70% | 38.00% | 0.34% | 0.00% | NA |
| Indica II | 465 | 64.70% | 35.30% | 0.00% | 0.00% | NA |
| Indica III | 913 | 55.80% | 44.10% | 0.00% | 0.00% | T: 0.11% |
| Indica Intermediate | 786 | 65.30% | 34.50% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 93.90% | 6.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 98.40% | 1.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 85.40% | 14.60% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 86.70% | 13.30% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1212722921 | G -> A | LOC_Os12g22540.1 | synonymous_variant ; p.Gln58Gln; LOW | synonymous_codon | Average:56.689; most accessible tissue: Minghui63 young leaf, score: 78.821 | N | N | N | N |
| vg1212722921 | G -> T | LOC_Os12g22540.1 | missense_variant ; p.Gln58His; MODERATE | nonsynonymous_codon ; Q58H | Average:56.689; most accessible tissue: Minghui63 young leaf, score: 78.821 | probably damaging  |
2.213 |
DELETERIOUS | 0.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1212722921 | NA | 1.57E-06 | mr1677 | 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 |
| vg1212722921 | NA | 1.78E-06 | mr1363_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 |
| vg1212722921 | NA | 1.82E-06 | mr1925_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 |