Search for Variation information by Variation ID:

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

Detailed information for vg0314672341:

Variant ID: vg0314672341 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 14672341
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: 119. )

Flanking Sequence (100 bp) in Reference Genome:


CTAAAATCTGCAGTTTTGTGATAAATTTGGTGCTAAATGTGTAGTTTTGTGATACAACTCCTTAAATCTGTAGTTTTGTGATAATTTGGTCAAAATACCT[G/A]
TAGTTTTGTGAAATTTACTCATATTTTTATCATTGTGTAGATGGTAGATCTGAAGCTTCTAGATTGAAGATTACGCATAATGGATGACTGTGTTCATATA

Reverse complement sequence

TATATGAACACAGTCATCCATTATGCGTAATCTTCAATCTAGAAGCTTCAGATCTACCATCTACACAATGATAAAAATATGAGTAAATTTCACAAAACTA[C/T]
AGGTATTTTGACCAAATTATCACAAAACTACAGATTTAAGGAGTTGTATCACAAAACTACACATTTAGCACCAAATTTATCACAAAACTGCAGATTTTAG

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 99.50% 0.40% 0.08% 0.00% NA
All Indica  2759 99.30% 0.60% 0.11% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 98.30% 1.50% 0.22% 0.00% NA
Indica III  913 99.50% 0.30% 0.22% 0.00% NA
Indica Intermediate  786 99.50% 0.50% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 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
vg0314672341 G -> A LOC_Os03g25610.1 upstream_gene_variant ; 4066.0bp to feature; MODIFIER N Average:40.986; most accessible tissue: Minghui63 flag leaf, score: 58.568 N N N N
vg0314672341 G -> A LOC_Os03g25620.1 intron_variant ; MODIFIER N Average:40.986; most accessible tissue: Minghui63 flag leaf, score: 58.568 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0314672341 NA 2.32E-07 mr1310_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
vg0314672341 NA 9.01E-06 mr1322_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
vg0314672341 NA 7.83E-06 mr1470_2 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
vg0314672341 NA 3.36E-07 mr1498_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
vg0314672341 NA 6.90E-06 mr1719_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
vg0314672341 NA 2.54E-06 mr1879_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
vg0314672341 NA 8.96E-07 mr1925_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