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Detailed information for vg0225037147:

Variant ID: vg0225037147 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 25037147
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCTCGCTGTTGATGAATTTGATTAGTGGGATGCGCCAGTCATCTGTGGTCTCGATATCGGCAACGGCGCGTTCTGCCTTTGTGGCCTCCGAGCCAATGTC[G/A]
GGGGTGGCCGGGCTAACTTCGCCGCTAACCTCTTTTACTGATGGCTTCGTCAGGATGTCTAGAAAAGTGTCGGGTTCGAGCGGTTCTCGTCTGGACGCAC

Reverse complement sequence

GTGCGTCCAGACGAGAACCGCTCGAACCCGACACTTTTCTAGACATCCTGACGAAGCCATCAGTAAAAGAGGTTAGCGGCGAAGTTAGCCCGGCCACCCC[C/T]
GACATTGGCTCGGAGGCCACAAAGGCAGAACGCGCCGTTGCCGATATCGAGACCACAGATGACTGGCGCATCCCACTAATCAAATTCATCAACAGCGAGG

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 94.40% 4.30% 0.06% 1.25% NA
All Indica  2759 93.70% 4.10% 0.11% 2.14% NA
All Japonica  1512 99.20% 0.80% 0.00% 0.00% NA
Aus  269 95.90% 4.10% 0.00% 0.00% NA
Indica I  595 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 96.80% 3.20% 0.00% 0.00% NA
Indica III  913 88.20% 5.40% 0.33% 6.13% NA
Indica Intermediate  786 93.80% 5.90% 0.00% 0.38% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 98.20% 1.80% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 40.60% 59.40% 0.00% 0.00% NA
Intermediate  90 86.70% 13.30% 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
vg0225037147 G -> A LOC_Os02g41696.1 synonymous_variant ; p.Pro154Pro; LOW synonymous_codon Average:31.361; most accessible tissue: Zhenshan97 root, score: 41.416 N N N N
vg0225037147 G -> DEL LOC_Os02g41696.1 N frameshift_variant Average:31.361; most accessible tissue: Zhenshan97 root, score: 41.416 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0225037147 NA 6.24E-06 mr1099 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
vg0225037147 2.05E-06 2.10E-06 mr1101 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
vg0225037147 2.99E-06 3.13E-06 mr1868 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
vg0225037147 4.77E-06 NA 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
vg0225037147 3.59E-06 2.16E-06 mr1123_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
vg0225037147 9.71E-06 NA mr1150_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