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Detailed information for vg0235865062:

Variant ID: vg0235865062 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 35865062
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAGACCCGTCTGGGAAAGACTCTGACCCGACTAACATGGACACAAGTTCTTCCAAAGAAACCGGACCAACTGCTAAGGATCATCCGAGTGACAATCAGCC[A/G]
GCAACCGACAATGTAGAACCCAGCAACGAGCCCCCGACTGGGAACCAGCCGGCCGAAGCTGAAGTCGGTGCTGGCCAGGAGCCCCCGACTGGAAACCAGT

Reverse complement sequence

ACTGGTTTCCAGTCGGGGGCTCCTGGCCAGCACCGACTTCAGCTTCGGCCGGCTGGTTCCCAGTCGGGGGCTCGTTGCTGGGTTCTACATTGTCGGTTGC[T/C]
GGCTGATTGTCACTCGGATGATCCTTAGCAGTTGGTCCGGTTTCTTTGGAAGAACTTGTGTCCATGTTAGTCGGGTCAGAGTCTTTCCCAGACGGGTCTA

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 85.10% 12.40% 2.50% 0.00% NA
All Indica  2759 99.30% 0.40% 0.25% 0.00% NA
All Japonica  1512 57.40% 35.60% 6.94% 0.00% NA
Aus  269 94.40% 5.20% 0.37% 0.00% NA
Indica I  595 99.50% 0.20% 0.34% 0.00% NA
Indica II  465 99.10% 0.60% 0.22% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 98.70% 0.80% 0.51% 0.00% NA
Temperate Japonica  767 33.50% 58.80% 7.69% 0.00% NA
Tropical Japonica  504 86.50% 7.50% 5.95% 0.00% NA
Japonica Intermediate  241 72.60% 20.70% 6.64% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 77.80% 16.70% 5.56% 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
vg0235865062 A -> G LOC_Os02g58700.1 synonymous_variant ; p.Pro407Pro; LOW synonymous_codon Average:40.63; most accessible tissue: Zhenshan97 flag leaf, score: 54.545 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0235865062 NA 1.21E-09 Heading_date All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0235865062 3.45E-06 3.45E-06 mr1186_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
vg0235865062 NA 4.73E-06 mr1359_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
vg0235865062 NA 4.98E-06 mr1627_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
vg0235865062 NA 8.75E-06 mr1647_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
vg0235865062 NA 5.63E-06 mr1648_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
vg0235865062 NA 5.44E-08 mr1709_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
vg0235865062 NA 6.80E-06 mr1977_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
vg0235865062 NA 2.43E-06 mr1977_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