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Detailed information for vg1004778450:

Variant ID: vg1004778450 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 4778450
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, A: 0.01, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:


TCGTATGTGTAGCTGCACGACTCCGAACACCACAAGAACCATGTATCATTCAAAATTTTCTTATTACTGCTCATCAAAATAGAGATCGATGCGATCAATT[C/A]
AATGAGAACGACTTGATTAAAACACGTTTGCGAACTCGATAATGTCTATGTTTTTGGAGGGGATGTCCATATTGGCTGGAACGTCAATTTCAGATCTGCA

Reverse complement sequence

TGCAGATCTGAAATTGACGTTCCAGCCAATATGGACATCCCCTCCAAAAACATAGACATTATCGAGTTCGCAAACGTGTTTTAATCAAGTCGTTCTCATT[G/T]
AATTGATCGCATCGATCTCTATTTTGATGAGCAGTAATAAGAAAATTTTGAATGATACATGGTTCTTGTGGTGTTCGGAGTCGTGCAGCTACACATACGA

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 80.00% 19.70% 0.00% 0.21% NA
All Indica  2759 66.50% 33.20% 0.00% 0.33% NA
All Japonica  1512 99.30% 0.70% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 82.40% 17.50% 0.00% 0.17% NA
Indica II  465 69.20% 30.30% 0.00% 0.43% NA
Indica III  913 60.90% 38.80% 0.00% 0.33% NA
Indica Intermediate  786 59.30% 40.30% 0.00% 0.38% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 97.50% 2.50% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 91.10% 7.80% 0.00% 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
vg1004778450 C -> A LOC_Os10g08840.1 upstream_gene_variant ; 4793.0bp to feature; MODIFIER silent_mutation Average:50.106; most accessible tissue: Zhenshan97 young leaf, score: 68.794 N N N N
vg1004778450 C -> A LOC_Os10g08840.2 upstream_gene_variant ; 4793.0bp to feature; MODIFIER silent_mutation Average:50.106; most accessible tissue: Zhenshan97 young leaf, score: 68.794 N N N N
vg1004778450 C -> A LOC_Os10g08830.1 intron_variant ; MODIFIER silent_mutation Average:50.106; most accessible tissue: Zhenshan97 young leaf, score: 68.794 N N N N
vg1004778450 C -> DEL N N silent_mutation Average:50.106; most accessible tissue: Zhenshan97 young leaf, score: 68.794 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1004778450 NA 1.33E-08 mr1707 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
vg1004778450 NA 4.40E-09 mr1707_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
vg1004778450 NA 4.01E-09 mr1860_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