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Detailed information for vg0321955285:

Variant ID: vg0321955285 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 21955285
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGCTGGGAGCAATCTGCTCCTCCGTTGTCACCGCACATAACACCATAGTCGTTCAGGTATGCTGCTGAATTTCTTCCTTTTCAGTTTGCTCTCTTCGGCT[G/A]
ATCGGCTCCTATGCGGGCTTCTGAGATAAGGAGGAGAAGAAATGATTAGGCTGACGCCAGTAAAATTTCTCTCTTTAACAAAAGCGTTCTATGTGCTTGG

Reverse complement sequence

CCAAGCACATAGAACGCTTTTGTTAAAGAGAGAAATTTTACTGGCGTCAGCCTAATCATTTCTTCTCCTCCTTATCTCAGAAGCCCGCATAGGAGCCGAT[C/T]
AGCCGAAGAGAGCAAACTGAAAAGGAAGAAATTCAGCAGCATACCTGAACGACTATGGTGTTATGTGCGGTGACAACGGAGGAGCAGATTGCTCCCAGCG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.20% 3.80% 0.02% 0.00% NA
All Indica  2759 98.70% 1.30% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.00% 0.07% 0.00% NA
Aus  269 49.10% 50.90% 0.00% 0.00% NA
Indica I  595 98.00% 2.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 96.90% 3.10% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0321955285 G -> A LOC_Os03g39520.1 upstream_gene_variant ; 2223.0bp to feature; MODIFIER silent_mutation Average:44.637; most accessible tissue: Zhenshan97 flower, score: 66.841 N N N N
vg0321955285 G -> A LOC_Os03g39540.1 downstream_gene_variant ; 4648.0bp to feature; MODIFIER silent_mutation Average:44.637; most accessible tissue: Zhenshan97 flower, score: 66.841 N N N N
vg0321955285 G -> A LOC_Os03g39530.1 intron_variant ; MODIFIER silent_mutation Average:44.637; most accessible tissue: Zhenshan97 flower, score: 66.841 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0321955285 2.44E-06 NA mr1150 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
vg0321955285 NA 1.23E-09 mr1317_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
vg0321955285 NA 3.46E-06 mr1603_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
vg0321955285 NA 5.86E-06 mr1608_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
vg0321955285 NA 1.64E-10 mr1818_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