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Detailed information for vg0905694212:

Variant ID: vg0905694212 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 5694212
Reference Allele: CAlternative Allele: G
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTTCGGAAGTTCCAAAAATTTTCGGAATTATTTTCGGAAGTTCCGAAAATTCCTGGCCGAGCCCTCCAACCTTGGTTTCGAATGATTCTTGCCTCCAAT[C/G]
ACTTGTACATCTTCTCTTTGGCTTCTGAAAAGGTCAATTAGGCCTAGAGGGGGGGGGTGAATAGGCTAATTTAAAAACTTAAGGAAAGCGGAAGCAGTAA

Reverse complement sequence

TTACTGCTTCCGCTTTCCTTAAGTTTTTAAATTAGCCTATTCACCCCCCCCCTCTAGGCCTAATTGACCTTTTCAGAAGCCAAAGAGAAGATGTACAAGT[G/C]
ATTGGAGGCAAGAATCATTCGAAACCAAGGTTGGAGGGCTCGGCCAGGAATTTTCGGAACTTCCGAAAATAATTCCGAAAATTTTTGGAACTTCCGAAAA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 49.60% 41.50% 0.42% 8.48% NA
All Indica  2759 80.20% 17.40% 0.65% 1.67% NA
All Japonica  1512 1.30% 81.90% 0.00% 16.87% NA
Aus  269 29.00% 67.70% 0.37% 2.97% NA
Indica I  595 76.80% 21.50% 1.34% 0.34% NA
Indica II  465 65.20% 32.30% 1.08% 1.51% NA
Indica III  913 88.00% 9.40% 0.00% 2.63% NA
Indica Intermediate  786 82.80% 14.90% 0.64% 1.65% NA
Temperate Japonica  767 1.40% 91.30% 0.00% 7.30% NA
Tropical Japonica  504 0.20% 82.50% 0.00% 17.26% NA
Japonica Intermediate  241 2.90% 50.60% 0.00% 46.47% NA
VI/Aromatic  96 8.30% 10.40% 0.00% 81.25% NA
Intermediate  90 28.90% 54.40% 1.11% 15.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0905694212 C -> G LOC_Os09g10430.1 upstream_gene_variant ; 3525.0bp to feature; MODIFIER silent_mutation Average:18.64; most accessible tissue: Callus, score: 37.11 N N N N
vg0905694212 C -> G LOC_Os09g10410.1 downstream_gene_variant ; 1594.0bp to feature; MODIFIER silent_mutation Average:18.64; most accessible tissue: Callus, score: 37.11 N N N N
vg0905694212 C -> G LOC_Os09g10420.1 downstream_gene_variant ; 1896.0bp to feature; MODIFIER silent_mutation Average:18.64; most accessible tissue: Callus, score: 37.11 N N N N
vg0905694212 C -> G LOC_Os09g10410-LOC_Os09g10420 intergenic_region ; MODIFIER silent_mutation Average:18.64; most accessible tissue: Callus, score: 37.11 N N N N
vg0905694212 C -> DEL N N silent_mutation Average:18.64; most accessible tissue: Callus, score: 37.11 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0905694212 NA 2.73E-06 mr1113 Ind_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
vg0905694212 NA 8.56E-07 mr1748 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
vg0905694212 NA 8.38E-06 mr1771 Ind_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
vg0905694212 NA 3.51E-06 mr1944 Ind_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