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Detailed information for vg0135250174:

Variant ID: vg0135250174 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 35250174
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.73, T: 0.28, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


GAAAACGGAGCGGATACGGATGGATAATGCTCATACCATATTCGTTTTCATATTTTTTTACCGGATACGAAAACGAATACGGATAGCTCGAATACGGAAA[C/T]
AAATACGGATTATCTCGAATACGAATAAGAATCGAATATGATCGGACATGAATACGGAAACAATTTTTTCTCAGAACACGAAAACCAACTCAACTTCTAA

Reverse complement sequence

TTAGAAGTTGAGTTGGTTTTCGTGTTCTGAGAAAAAATTGTTTCCGTATTCATGTCCGATCATATTCGATTCTTATTCGTATTCGAGATAATCCGTATTT[G/A]
TTTCCGTATTCGAGCTATCCGTATTCGTTTTCGTATCCGGTAAAAAAATATGAAAACGAATATGGTATGAGCATTATCCATCCGTATCCGCTCCGTTTTC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 80.90% 15.50% 2.58% 0.95% NA
All Indica  2759 96.30% 1.50% 0.58% 1.59% NA
All Japonica  1512 53.40% 41.10% 5.56% 0.00% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 96.10% 3.70% 0.17% 0.00% NA
Indica II  465 92.00% 0.00% 1.29% 6.67% NA
Indica III  913 99.70% 0.10% 0.22% 0.00% NA
Indica Intermediate  786 95.20% 2.30% 0.89% 1.65% NA
Temperate Japonica  767 66.60% 28.30% 5.08% 0.00% NA
Tropical Japonica  504 35.70% 57.30% 6.94% 0.00% NA
Japonica Intermediate  241 48.10% 47.70% 4.15% 0.00% NA
VI/Aromatic  96 29.20% 50.00% 20.83% 0.00% NA
Intermediate  90 71.10% 26.70% 1.11% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0135250174 C -> T LOC_Os01g60930.1 downstream_gene_variant ; 3366.0bp to feature; MODIFIER silent_mutation Average:41.402; most accessible tissue: Zhenshan97 panicle, score: 68.538 N N N N
vg0135250174 C -> T LOC_Os01g60940.1 downstream_gene_variant ; 1248.0bp to feature; MODIFIER silent_mutation Average:41.402; most accessible tissue: Zhenshan97 panicle, score: 68.538 N N N N
vg0135250174 C -> T LOC_Os01g60940-LOC_Os01g60960 intergenic_region ; MODIFIER silent_mutation Average:41.402; most accessible tissue: Zhenshan97 panicle, score: 68.538 N N N N
vg0135250174 C -> DEL N N silent_mutation Average:41.402; most accessible tissue: Zhenshan97 panicle, score: 68.538 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0135250174 1.50E-06 NA mr1712 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
vg0135250174 NA 1.01E-06 mr1712 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
vg0135250174 NA 6.73E-06 mr1826_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