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Detailed information for vg0233808913:

Variant ID: vg0233808913 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 33808913
Reference Allele: GAlternative Allele: A
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: 313. )

Flanking Sequence (100 bp) in Reference Genome:


GATGAATGCAAAAGTTAAATTAACATGAGAACTTACTATCATGCTATTATGATCATATTAACAACAAAACACAACCTCCAGATCCTTTTTGGGCAATTTC[G/A]
AGAGGAATTCAGCACTTTCTTCATAGTAAGTGATTGCTGAAGGAGCATCTCCCAAGGTCCGACTGTGGCATGGAATGAGGTCAATTATGAACAAACAAAG

Reverse complement sequence

CTTTGTTTGTTCATAATTGACCTCATTCCATGCCACAGTCGGACCTTGGGAGATGCTCCTTCAGCAATCACTTACTATGAAGAAAGTGCTGAATTCCTCT[C/T]
GAAATTGCCCAAAAAGGATCTGGAGGTTGTGTTTTGTTGTTAATATGATCATAATAGCATGATAGTAAGTTCTCATGTTAATTTAACTTTTGCATTCATC

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 99.40% 0.40% 0.23% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 98.10% 1.20% 0.66% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 96.70% 2.00% 1.30% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 98.90% 0.00% 1.11% 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
vg0233808913 G -> A LOC_Os02g55200.1 missense_variant ; p.Ser243Leu; MODERATE nonsynonymous_codon ; S243L Average:44.083; most accessible tissue: Minghui63 flag leaf, score: 64.284 possibly damaging 1.746 TOLERATED 0.13
vg0233808913 G -> A LOC_Os02g55200.2 missense_variant ; p.Ser243Leu; MODERATE nonsynonymous_codon ; S243L Average:44.083; most accessible tissue: Minghui63 flag leaf, score: 64.284 possibly damaging 1.746 TOLERATED 0.13

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0233808913 8.13E-07 4.80E-07 mr1038_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
vg0233808913 6.14E-08 6.14E-08 mr1389_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