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Detailed information for vg0230277888:

Variant ID: vg0230277888 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 30277888
Reference Allele: CAlternative Allele: G
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, G: 0.06, others allele: 0.00, population size: 191. )

Flanking Sequence (100 bp) in Reference Genome:


AGTAAATTTCACAAAACTACAGGTATTTTGACCAAATTATCACAAAACTACAGATTTAAGGAGTTGTATCACAAAACTACACATTTAGCACCAAATTTAT[C/G]
ACAAAACTACATATTTTAGGTTAAGTATCACAAAAATGCATATTTAATATTGAACTTATCACAAAACTACAACTTTTAGAGTTTAAATCCTAGCACTATT

Reverse complement sequence

AATAGTGCTAGGATTTAAACTCTAAAAGTTGTAGTTTTGTGATAAGTTCAATATTAAATATGCATTTTTGTGATACTTAACCTAAAATATGTAGTTTTGT[G/C]
ATAAATTTGGTGCTAAATGTGTAGTTTTGTGATACAACTCCTTAAATCTGTAGTTTTGTGATAATTTGGTCAAAATACCTGTAGTTTTGTGAAATTTACT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 63.10% 36.90% 0.00% 0.00% NA
All Indica  2759 97.90% 2.10% 0.00% 0.00% NA
All Japonica  1512 0.90% 99.10% 0.00% 0.00% NA
Aus  269 86.20% 13.80% 0.00% 0.00% NA
Indica I  595 99.00% 1.00% 0.00% 0.00% NA
Indica II  465 96.30% 3.70% 0.00% 0.00% NA
Indica III  913 98.90% 1.10% 0.00% 0.00% NA
Indica Intermediate  786 96.70% 3.30% 0.00% 0.00% NA
Temperate Japonica  767 0.40% 99.60% 0.00% 0.00% NA
Tropical Japonica  504 1.40% 98.60% 0.00% 0.00% NA
Japonica Intermediate  241 1.70% 98.30% 0.00% 0.00% NA
VI/Aromatic  96 3.10% 96.90% 0.00% 0.00% NA
Intermediate  90 34.40% 65.60% 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
vg0230277888 C -> G LOC_Os02g49550.1 upstream_gene_variant ; 4470.0bp to feature; MODIFIER silent_mutation Average:41.196; most accessible tissue: Zhenshan97 panicle, score: 61.671 N N N N
vg0230277888 C -> G LOC_Os02g49540.1 downstream_gene_variant ; 3413.0bp to feature; MODIFIER silent_mutation Average:41.196; most accessible tissue: Zhenshan97 panicle, score: 61.671 N N N N
vg0230277888 C -> G LOC_Os02g49530.1 intron_variant ; MODIFIER silent_mutation Average:41.196; most accessible tissue: Zhenshan97 panicle, score: 61.671 N N N N
vg0230277888 C -> G LOC_Os02g49530.2 intron_variant ; MODIFIER silent_mutation Average:41.196; most accessible tissue: Zhenshan97 panicle, score: 61.671 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0230277888 5.64E-08 NA Awn_length Ind_All YES 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
vg0230277888 NA 1.18E-08 mr1050 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
vg0230277888 NA 1.57E-10 mr1272 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
vg0230277888 NA 1.89E-23 mr1571 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
vg0230277888 NA 1.72E-10 mr1775 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