Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0826524537:

Variant ID: vg0826524537 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 26524537
Reference Allele: CAlternative Allele: A,T
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


GATGTATCTATCACGTTTGTGTATATCTATTGGATAAATAGGTTTTTCTTATTATCTTCAATCCTATATTGTGTCGGTTAGGTTCGATCTATTAGATTGT[C/A,T]
GCTAATAAGTTTTATTCTACTAAGCCAATAGGTTTTCATGCAACGTTTCATCGGAGTCTAGCCAATGAGTTATCTTGTTACTTTTTTAAGTGTTGTATCG

Reverse complement sequence

CGATACAACACTTAAAAAAGTAACAAGATAACTCATTGGCTAGACTCCGATGAAACGTTGCATGAAAACCTATTGGCTTAGTAGAATAAAACTTATTAGC[G/T,A]
ACAATCTAATAGATCGAACCTAACCGACACAATATAGGATTGAAGATAATAAGAAAAACCTATTTATCCAATAGATATACACAAACGTGATAGATACATC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.70% 1.70% 0.47% 0.00% T: 0.06%
All Indica  2759 99.90% 0.00% 0.00% 0.00% T: 0.11%
All Japonica  1512 93.30% 5.40% 1.39% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.70% 0.00% 0.00% 0.00% T: 0.34%
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 99.90% 0.00% 0.00% 0.00% T: 0.13%
Temperate Japonica  767 94.70% 3.70% 1.69% 0.00% NA
Tropical Japonica  504 96.60% 3.20% 0.20% 0.00% NA
Japonica Intermediate  241 81.70% 15.40% 2.90% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 1.10% 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
vg0826524537 C -> T LOC_Os08g41960.1 intron_variant ; MODIFIER silent_mutation Average:32.075; most accessible tissue: Zhenshan97 young leaf, score: 46.636 N N N N
vg0826524537 C -> A LOC_Os08g41960.1 intron_variant ; MODIFIER silent_mutation Average:32.075; most accessible tissue: Zhenshan97 young leaf, score: 46.636 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0826524537 2.73E-06 2.73E-06 mr1191 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