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Detailed information for vg0321930604:

Variant ID: vg0321930604 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 21930604
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCGCAGGTTTGCTGCAGCCTTTAAAGATACCAGAATGGAAGTGGGAGGAAATTGGGATGGATTTCATCACTGGTCTGCCCAGAATGTCATCTGGCCATGA[T/C]
TCTATTTGGGTGATAGTCGACAGGCTTACAAAAGTTGCTCATTGCATCCCTGTGAGGACAACATATTCCGGAAATCGTTTGGCAGAATTGTATATGGCAA

Reverse complement sequence

TTGCCATATACAATTCTGCCAAACGATTTCCGGAATATGTTGTCCTCACAGGGATGCAATGAGCAACTTTTGTAAGCCTGTCGACTATCACCCAAATAGA[A/G]
TCATGGCCAGATGACATTCTGGGCAGACCAGTGATGAAATCCATCCCAATTTCCTCCCACTTCCATTCTGGTATCTTTAAAGGCTGCAGCAAACCTGCGG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 88.60% 0.00% 2.60% 8.80% NA
All Indica  2759 82.00% 0.10% 4.13% 13.77% NA
All Japonica  1512 99.00% 0.00% 0.07% 0.93% NA
Aus  269 93.70% 0.00% 2.23% 4.09% NA
Indica I  595 78.30% 0.00% 5.88% 15.80% NA
Indica II  465 72.00% 0.20% 4.73% 23.01% NA
Indica III  913 90.30% 0.10% 1.75% 7.89% NA
Indica Intermediate  786 81.20% 0.00% 5.22% 13.61% NA
Temperate Japonica  767 99.70% 0.00% 0.00% 0.26% NA
Tropical Japonica  504 97.40% 0.00% 0.20% 2.38% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 0.00% 1.04% NA
Intermediate  90 86.70% 0.00% 2.22% 11.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0321930604 T -> C LOC_Os03g39460.1 upstream_gene_variant ; 2129.0bp to feature; MODIFIER silent_mutation Average:21.26; most accessible tissue: Zhenshan97 root, score: 32.766 N N N N
vg0321930604 T -> C LOC_Os03g39490.1 upstream_gene_variant ; 3111.0bp to feature; MODIFIER silent_mutation Average:21.26; most accessible tissue: Zhenshan97 root, score: 32.766 N N N N
vg0321930604 T -> C LOC_Os03g39450.1 downstream_gene_variant ; 3647.0bp to feature; MODIFIER silent_mutation Average:21.26; most accessible tissue: Zhenshan97 root, score: 32.766 N N N N
vg0321930604 T -> C LOC_Os03g39460-LOC_Os03g39490 intergenic_region ; MODIFIER silent_mutation Average:21.26; most accessible tissue: Zhenshan97 root, score: 32.766 N N N N
vg0321930604 T -> DEL N N silent_mutation Average:21.26; most accessible tissue: Zhenshan97 root, score: 32.766 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0321930604 3.62E-06 NA mr1095_2 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
vg0321930604 7.65E-06 5.55E-06 mr1098_2 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
vg0321930604 5.68E-06 NA mr1563_2 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