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Detailed information for vg1213936261:

Variant ID: vg1213936261 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 13936261
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, G: 0.05, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:


AGGTTTAGAACCAGGCAGAGGTGCAGCCCACCTCCTGCCGACTATATCATACGCGATGTGCAGTAAAAACCCTAAAAAAATTTTCCCTAACTACACCGAA[C/G]
AAAACTTCAAAGCACACACATCATGTGGTTTCAGATCCAGGATGCTTTACTCGACATTGGGCAAAATCAACTCAAAAACATATACCCAGTAAACTCCAAA

Reverse complement sequence

TTTGGAGTTTACTGGGTATATGTTTTTGAGTTGATTTTGCCCAATGTCGAGTAAAGCATCCTGGATCTGAAACCACATGATGTGTGTGCTTTGAAGTTTT[G/C]
TTCGGTGTAGTTAGGGAAAATTTTTTTAGGGTTTTTACTGCACATCGCGTATGATATAGTCGGCAGGAGGTGGGCTGCACCTCTGCCTGGTTCTAAACCT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 53.30% 19.00% 27.66% 0.00% NA
All Indica  2759 47.80% 26.80% 25.37% 0.00% NA
All Japonica  1512 57.10% 8.30% 34.66% 0.00% NA
Aus  269 82.50% 2.60% 14.87% 0.00% NA
Indica I  595 29.10% 40.80% 30.08% 0.00% NA
Indica II  465 70.80% 10.50% 18.71% 0.00% NA
Indica III  913 46.90% 29.20% 23.88% 0.00% NA
Indica Intermediate  786 49.50% 23.00% 27.48% 0.00% NA
Temperate Japonica  767 84.20% 2.50% 13.30% 0.00% NA
Tropical Japonica  504 24.60% 14.90% 60.52% 0.00% NA
Japonica Intermediate  241 38.60% 12.90% 48.55% 0.00% NA
VI/Aromatic  96 67.70% 13.50% 18.75% 0.00% NA
Intermediate  90 57.80% 14.40% 27.78% 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
vg1213936261 C -> G LOC_Os12g24410.1 upstream_gene_variant ; 3699.0bp to feature; MODIFIER silent_mutation Average:29.709; most accessible tissue: Minghui63 young leaf, score: 42.042 N N N N
vg1213936261 C -> G LOC_Os12g24430.1 upstream_gene_variant ; 2534.0bp to feature; MODIFIER silent_mutation Average:29.709; most accessible tissue: Minghui63 young leaf, score: 42.042 N N N N
vg1213936261 C -> G LOC_Os12g24420.1 downstream_gene_variant ; 280.0bp to feature; MODIFIER silent_mutation Average:29.709; most accessible tissue: Minghui63 young leaf, score: 42.042 N N N N
vg1213936261 C -> G LOC_Os12g24410-LOC_Os12g24420 intergenic_region ; MODIFIER silent_mutation Average:29.709; most accessible tissue: Minghui63 young leaf, score: 42.042 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1213936261 NA 4.41E-06 mr1364 Jap_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
vg1213936261 NA 3.48E-09 mr1401 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
vg1213936261 NA 2.51E-06 mr1443 Jap_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
vg1213936261 NA 1.09E-06 mr1602 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