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Detailed information for vg0316595932:

Variant ID: vg0316595932 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 16595932
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCATTATTATGTGCAAACCAAAACCATATGTAAGTATGAGTCCGGATTGGTAATTGGGTATCTTGAATCATGTTGTGAGTAATAGATCTTAGAGCAGTCA[G/C]
AAATCTATCTATATTAACTTATTAAAGAAATAGAAAAAGGAGCCTCCACGTTCGCTCTCACGGTCTAAAAATTCTTATATTAATCGGAGAAAAAGAAAAC

Reverse complement sequence

GTTTTCTTTTTCTCCGATTAATATAAGAATTTTTAGACCGTGAGAGCGAACGTGGAGGCTCCTTTTTCTATTTCTTTAATAAGTTAATATAGATAGATTT[C/G]
TGACTGCTCTAAGATCTATTACTCACAACATGATTCAAGATACCCAATTACCAATCCGGACTCATACTTACATATGGTTTTGGTTTGCACATAATAATGA

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 92.00% 7.90% 0.19% 0.00% NA
All Indica  2759 97.10% 2.80% 0.04% 0.00% NA
All Japonica  1512 85.60% 14.00% 0.40% 0.00% NA
Aus  269 74.30% 25.30% 0.37% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 97.80% 2.20% 0.00% 0.00% NA
Indica Intermediate  786 92.90% 7.00% 0.13% 0.00% NA
Temperate Japonica  767 93.90% 5.90% 0.26% 0.00% NA
Tropical Japonica  504 89.50% 10.50% 0.00% 0.00% NA
Japonica Intermediate  241 51.00% 47.30% 1.66% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 91.10% 7.80% 1.11% 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
vg0316595932 G -> C LOC_Os03g29190.1 3_prime_UTR_variant ; 288.0bp to feature; MODIFIER silent_mutation Average:59.336; most accessible tissue: Minghui63 root, score: 73.73 N N N N
vg0316595932 G -> C LOC_Os03g29190.2 3_prime_UTR_variant ; 288.0bp to feature; MODIFIER silent_mutation Average:59.336; most accessible tissue: Minghui63 root, score: 73.73 N N N N
vg0316595932 G -> C LOC_Os03g29194.1 downstream_gene_variant ; 3667.0bp to feature; MODIFIER silent_mutation Average:59.336; most accessible tissue: Minghui63 root, score: 73.73 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0316595932 NA 8.11E-06 mr1117 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
vg0316595932 NA 9.18E-06 mr1240 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
vg0316595932 NA 2.91E-07 mr1117_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
vg0316595932 NA 2.33E-06 mr1119_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
vg0316595932 5.61E-08 5.61E-08 mr1197_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
vg0316595932 NA 4.43E-07 mr1240_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
vg0316595932 NA 2.00E-07 mr1496_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
vg0316595932 NA 3.97E-06 mr1961_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