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Detailed information for vg0134236950:

Variant ID: vg0134236950 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 34236950
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.01, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


TTGAACCCGGTCTAACCGTCCAAACTCCGCAGTCTAACCAGTCCGTCGGTCTGACCACCCTGCCGGCCCAGTTTAACCGTCATACATGCACACCTCACGC[G/A]
CCTTCTCCGGAGCCGTATACTCACCGCATCACCTTGATCACCACAAAGCTGCACCATGCCTCTCGTCTTGTGCCCGTGAGCCACGCCGCCAAAACAACGT

Reverse complement sequence

ACGTTGTTTTGGCGGCGTGGCTCACGGGCACAAGACGAGAGGCATGGTGCAGCTTTGTGGTGATCAAGGTGATGCGGTGAGTATACGGCTCCGGAGAAGG[C/T]
GCGTGAGGTGTGCATGTATGACGGTTAAACTGGGCCGGCAGGGTGGTCAGACCGACGGACTGGTTAGACTGCGGAGTTTGGACGGTTAGACCGGGTTCAA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 78.20% 21.00% 0.00% 0.76% NA
All Indica  2759 98.00% 2.00% 0.00% 0.00% NA
All Japonica  1512 37.20% 60.40% 0.00% 2.38% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 96.50% 3.50% 0.00% 0.00% NA
Indica II  465 99.10% 0.90% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 96.10% 3.90% 0.00% 0.00% NA
Temperate Japonica  767 8.70% 87.00% 0.00% 4.30% NA
Tropical Japonica  504 68.10% 31.70% 0.00% 0.20% NA
Japonica Intermediate  241 63.10% 36.10% 0.00% 0.83% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 74.40% 25.60% 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
vg0134236950 G -> A LOC_Os01g59230.1 intron_variant ; MODIFIER silent_mutation Average:66.053; most accessible tissue: Zhenshan97 flower, score: 80.159 N N N N
vg0134236950 G -> DEL N N silent_mutation Average:66.053; most accessible tissue: Zhenshan97 flower, score: 80.159 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0134236950 NA 1.29E-12 mr1010 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
vg0134236950 NA 5.77E-06 mr1503 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
vg0134236950 8.12E-06 NA mr1679 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
vg0134236950 2.62E-06 NA mr1691 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
vg0134236950 NA 1.48E-07 mr1180_2 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