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Detailed information for vg0310049531:

Variant ID: vg0310049531 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 10049531
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTCTATTCTAATTAAATGCATGCATAGATTGAATTTATCCGAGTGATCCAAATGAAAAGGTAATAATAATAATTTCTGGGTCTTTACGTTAGTTATGGTT[G/A]
TGCCTTATATTTTGGGATGGATGAAATATCGTTTTAGACATAATATCATTTACCAACAATTAATTAATTAAATTAGGTGGTTGTGTGTTTTATGACAGAA

Reverse complement sequence

TTCTGTCATAAAACACACAACCACCTAATTTAATTAATTAATTGTTGGTAAATGATATTATGTCTAAAACGATATTTCATCCATCCCAAAATATAAGGCA[C/T]
AACCATAACTAACGTAAAGACCCAGAAATTATTATTATTACCTTTTCATTTGGATCACTCGGATAAATTCAATCTATGCATGCATTTAATTAGAATAGAG

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 92.10% 6.70% 1.21% 0.00% NA
All Indica  2759 99.80% 0.10% 0.07% 0.00% NA
All Japonica  1512 76.90% 19.60% 3.51% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.30% 0.13% 0.00% NA
Temperate Japonica  767 95.40% 0.10% 4.43% 0.00% NA
Tropical Japonica  504 45.20% 52.60% 2.18% 0.00% NA
Japonica Intermediate  241 83.80% 12.90% 3.32% 0.00% NA
VI/Aromatic  96 94.80% 5.20% 0.00% 0.00% NA
Intermediate  90 83.30% 14.40% 2.22% 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
vg0310049531 G -> A LOC_Os03g18040.1 downstream_gene_variant ; 3735.0bp to feature; MODIFIER silent_mutation Average:34.85; most accessible tissue: Callus, score: 70.714 N N N N
vg0310049531 G -> A LOC_Os03g18040-LOC_Os03g18050 intergenic_region ; MODIFIER silent_mutation Average:34.85; most accessible tissue: Callus, score: 70.714 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0310049531 NA 6.75E-06 mr1277 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
vg0310049531 NA 3.81E-15 mr1410 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
vg0310049531 NA 1.66E-11 mr1454 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
vg0310049531 NA 1.84E-08 mr1539 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
vg0310049531 NA 7.94E-06 mr1543 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
vg0310049531 NA 2.85E-08 mr1668 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
vg0310049531 3.93E-11 1.02E-21 mr1871 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
vg0310049531 9.89E-06 1.69E-10 mr1871 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
vg0310049531 NA 2.92E-09 mr1398_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
vg0310049531 NA 3.47E-14 mr1410_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
vg0310049531 NA 1.21E-08 mr1543_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
vg0310049531 NA 3.63E-07 mr1668_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
vg0310049531 NA 2.56E-07 mr1671_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
vg0310049531 NA 1.81E-12 mr1680_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
vg0310049531 NA 3.35E-15 mr1742_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
vg0310049531 1.83E-08 3.60E-25 mr1871_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
vg0310049531 NA 3.03E-09 mr1871_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