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Detailed information for vg0220941121:

Variant ID: vg0220941121 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 20941121
Reference Allele: GAlternative Allele: A,T
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:


CGGTGTGTTCGATTTTTTCGTCAACACGAGGACGTCCAAGTCAAGGTGGAGGCCCAAACCAATTTGACCTCGGGTGCAATTCGGAGTCCAGGACCAGTCT[G/A,T]
CACTAAAACAGGCGCCCAGGTCGCATACGTGCTCGCATTGGGGCGTTCTTTATATGGATGGAAAGCTAAGAAGATAACATTTCCAATGGTTCTGGTCCCA

Reverse complement sequence

TGGGACCAGAACCATTGGAAATGTTATCTTCTTAGCTTTCCATCCATATAAAGAACGCCCCAATGCGAGCACGTATGCGACCTGGGCGCCTGTTTTAGTG[C/T,A]
AGACTGGTCCTGGACTCCGAATTGCACCCGAGGTCAAATTGGTTTGGGCCTCCACCTTGACTTGGACGTCCTCGTGTTGACGAAAAAATCGAACACACCG

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 95.90% 4.00% 0.02% 0.00% T: 0.04%
All Indica  2759 99.20% 0.80% 0.00% 0.00% NA
All Japonica  1512 92.70% 7.10% 0.00% 0.00% T: 0.13%
Aus  269 78.80% 20.80% 0.37% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.10% 0.90% 0.00% 0.00% NA
Indica III  913 99.10% 0.90% 0.00% 0.00% NA
Indica Intermediate  786 98.70% 1.30% 0.00% 0.00% NA
Temperate Japonica  767 90.90% 9.10% 0.00% 0.00% NA
Tropical Japonica  504 93.70% 6.00% 0.00% 0.00% T: 0.40%
Japonica Intermediate  241 96.70% 3.30% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 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
vg0220941121 G -> A LOC_Os02g34900.1 intron_variant ; MODIFIER silent_mutation Average:44.1; most accessible tissue: Minghui63 young leaf, score: 69.4 N N N N
vg0220941121 G -> T LOC_Os02g34900.1 intron_variant ; MODIFIER silent_mutation Average:44.1; most accessible tissue: Minghui63 young leaf, score: 69.4 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0220941121 NA 9.70E-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
vg0220941121 NA 4.36E-06 mr1123 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
vg0220941121 NA 2.75E-06 mr1150 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
vg0220941121 NA 5.42E-06 mr1242 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
vg0220941121 NA 1.19E-06 mr1247 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
vg0220941121 4.98E-06 4.98E-06 mr1861 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
vg0220941121 7.46E-06 4.30E-07 mr1186_2 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
vg0220941121 3.93E-06 3.22E-06 mr1265_2 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
vg0220941121 NA 3.94E-06 mr1267_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
vg0220941121 NA 1.44E-07 mr1360_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
vg0220941121 6.85E-06 NA mr1794_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
vg0220941121 5.07E-06 4.51E-09 mr1851_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