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Detailed information for vg0717377650:

Variant ID: vg0717377650 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 17377650
Reference Allele: CAlternative Allele: A,T
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.58, C: 0.38, A: 0.04, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:


AGGGAGAGCACAACTTTTTACTGAAACCATTCCAGAGGAGGCCTCCATGGTTAATATATTAAATGGAAAAAAGAAGAAGTTTTAAAACTACAAGGCAGAC[C/A,T]
GCCATGAAGTTAGAAGTACTCTCTCCGGACCATTTAGGTTGTGTTCGGGAGGTAAGGCTGGGAACTCACCTTCCGCGCACGAAAAACGGAGCGGCGCATT

Reverse complement sequence

AATGCGCCGCTCCGTTTTTCGTGCGCGGAAGGTGAGTTCCCAGCCTTACCTCCCGAACACAACCTAAATGGTCCGGAGAGAGTACTTCTAACTTCATGGC[G/T,A]
GTCTGCCTTGTAGTTTTAAAACTTCTTCTTTTTTCCATTTAATATATTAACCATGGAGGCCTCCTCTGGAATGGTTTCAGTAAAAAGTTGTGCTCTCCCT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 61.80% 38.00% 0.15% 0.00% T: 0.08%
All Indica  2759 41.00% 58.70% 0.18% 0.00% T: 0.14%
All Japonica  1512 93.30% 6.60% 0.13% 0.00% NA
Aus  269 82.20% 17.80% 0.00% 0.00% NA
Indica I  595 48.20% 51.40% 0.34% 0.00% NA
Indica II  465 69.50% 30.50% 0.00% 0.00% NA
Indica III  913 22.10% 77.80% 0.00% 0.00% T: 0.11%
Indica Intermediate  786 40.50% 58.80% 0.38% 0.00% T: 0.38%
Temperate Japonica  767 99.50% 0.30% 0.26% 0.00% NA
Tropical Japonica  504 83.10% 16.90% 0.00% 0.00% NA
Japonica Intermediate  241 94.60% 5.40% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 73.30% 26.70% 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
vg0717377650 C -> A LOC_Os07g29580.1 downstream_gene_variant ; 1740.0bp to feature; MODIFIER silent_mutation Average:43.222; most accessible tissue: Callus, score: 60.075 N N N N
vg0717377650 C -> A LOC_Os07g29590.1 downstream_gene_variant ; 3588.0bp to feature; MODIFIER silent_mutation Average:43.222; most accessible tissue: Callus, score: 60.075 N N N N
vg0717377650 C -> A LOC_Os07g29580-LOC_Os07g29590 intergenic_region ; MODIFIER silent_mutation Average:43.222; most accessible tissue: Callus, score: 60.075 N N N N
vg0717377650 C -> T LOC_Os07g29580.1 downstream_gene_variant ; 1740.0bp to feature; MODIFIER silent_mutation Average:43.222; most accessible tissue: Callus, score: 60.075 N N N N
vg0717377650 C -> T LOC_Os07g29590.1 downstream_gene_variant ; 3588.0bp to feature; MODIFIER silent_mutation Average:43.222; most accessible tissue: Callus, score: 60.075 N N N N
vg0717377650 C -> T LOC_Os07g29580-LOC_Os07g29590 intergenic_region ; MODIFIER silent_mutation Average:43.222; most accessible tissue: Callus, score: 60.075 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0717377650 8.91E-07 8.91E-07 mr1877 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
vg0717377650 NA 4.75E-06 mr1211_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