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Detailed information for vg0420539514:

Variant ID: vg0420539514 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 20539514
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCAATATGATGTTAAATAGAAAATTAAAAATTTATAAATAGGTAGAACCAGAAACGGTAAAAAATAATACCACTCATATGGAAATGGTGCTCGGTCGACC[C/T]
GGAATTTCCGTGACTGTTTTCATCCCCAGTGGCAAAAAGGGAACAAGAAAAAAAATTAATTTGATTTTTTTCATATAGTTTGTAGATTAGCAATTGAAAA

Reverse complement sequence

TTTTCAATTGCTAATCTACAAACTATATGAAAAAAATCAAATTAATTTTTTTTCTTGTTCCCTTTTTGCCACTGGGGATGAAAACAGTCACGGAAATTCC[G/A]
GGTCGACCGAGCACCATTTCCATATGAGTGGTATTATTTTTTACCGTTTCTGGTTCTACCTATTTATAAATTTTTAATTTTCTATTTAACATCATATTGC

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 96.80% 2.60% 0.61% 0.00% NA
All Indica  2759 97.80% 2.10% 0.07% 0.00% NA
All Japonica  1512 94.40% 3.80% 1.79% 0.00% NA
Aus  269 98.50% 1.50% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 96.60% 3.40% 0.00% 0.00% NA
Indica III  913 97.80% 2.20% 0.00% 0.00% NA
Indica Intermediate  786 96.90% 2.90% 0.13% 0.00% NA
Temperate Japonica  767 89.40% 7.20% 3.39% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.40% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0420539514 C -> T LOC_Os04g33920.1 upstream_gene_variant ; 3607.0bp to feature; MODIFIER silent_mutation Average:52.135; most accessible tissue: Callus, score: 74.064 N N N N
vg0420539514 C -> T LOC_Os04g33900.1 downstream_gene_variant ; 4740.0bp to feature; MODIFIER silent_mutation Average:52.135; most accessible tissue: Callus, score: 74.064 N N N N
vg0420539514 C -> T LOC_Os04g33910.1 downstream_gene_variant ; 523.0bp to feature; MODIFIER silent_mutation Average:52.135; most accessible tissue: Callus, score: 74.064 N N N N
vg0420539514 C -> T LOC_Os04g33910-LOC_Os04g33920 intergenic_region ; MODIFIER silent_mutation Average:52.135; most accessible tissue: Callus, score: 74.064 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0420539514 NA 4.49E-06 mr1210 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
vg0420539514 NA 7.98E-06 mr1765 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
vg0420539514 NA 1.43E-06 mr1631_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
vg0420539514 7.80E-08 7.80E-08 mr1973_2 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