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Detailed information for vg0609907276:

Variant ID: vg0609907276 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 9907276
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCTAGGGTTATGTGGTAATTCGTGGAGGTGGAGGGAGACACTTCCGATATGGGCCTAGTCTATTACAAGGCCCAAGGCCTAAGTTCGGTTTCAGCAATAG[C/T]
ACTGTCTTGTTTTAGCGATTCCCGTTGACTCGAGATGAATTTGGACATGAGACTGAATGCGTTTGAAAGGTAGCGAGATAAGCTTTCCACGAAATCCAAG

Reverse complement sequence

CTTGGATTTCGTGGAAAGCTTATCTCGCTACCTTTCAAACGCATTCAGTCTCATGTCCAAATTCATCTCGAGTCAACGGGAATCGCTAAAACAAGACAGT[G/A]
CTATTGCTGAAACCGAACTTAGGCCTTGGGCCTTGTAATAGACTAGGCCCATATCGGAAGTGTCTCCCTCCACCTCCACGAATTACCACATAACCCTAGC

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 96.20% 3.70% 0.11% 0.00% NA
All Indica  2759 99.70% 0.30% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.07% 0.00% NA
Aus  269 39.00% 59.50% 1.49% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 98.90% 1.10% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0609907276 C -> T LOC_Os06g17080.1 upstream_gene_variant ; 1686.0bp to feature; MODIFIER silent_mutation Average:41.706; most accessible tissue: Zhenshan97 panicle, score: 65.386 N N N N
vg0609907276 C -> T LOC_Os06g17090.1 upstream_gene_variant ; 3462.0bp to feature; MODIFIER silent_mutation Average:41.706; most accessible tissue: Zhenshan97 panicle, score: 65.386 N N N N
vg0609907276 C -> T LOC_Os06g17100.1 downstream_gene_variant ; 4696.0bp to feature; MODIFIER silent_mutation Average:41.706; most accessible tissue: Zhenshan97 panicle, score: 65.386 N N N N
vg0609907276 C -> T LOC_Os06g17080-LOC_Os06g17090 intergenic_region ; MODIFIER silent_mutation Average:41.706; most accessible tissue: Zhenshan97 panicle, score: 65.386 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0609907276 NA 9.82E-07 mr1556 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
vg0609907276 NA 3.64E-08 mr1669 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
vg0609907276 5.06E-06 NA mr1114_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
vg0609907276 2.45E-06 NA mr1117_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
vg0609907276 2.05E-07 NA mr1119_2 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
vg0609907276 1.63E-06 NA mr1496_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