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Detailed information for vg1012424922:

Variant ID: vg1012424922 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 12424922
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.82, C: 0.17, others allele: 0.00, population size: 46. )

Flanking Sequence (100 bp) in Reference Genome:


CTACAGTTGTTAACAACATATAATCCTTATATCGATATAAATTTAAATCAAGTGATTGGGATAAATCGGTTGCCTTGCCGAGACAGTATAAATCACTTAG[A/C]
TCGAAATATATATTAACAACCGGATTATATATGTTTATAACATAGCCGATCAGATAGATCTAGCATGTATCGGCTAATACTCCGATACCACTCTATATTA

Reverse complement sequence

TAATATAGAGTGGTATCGGAGTATTAGCCGATACATGCTAGATCTATCTGATCGGCTATGTTATAAACATATATAATCCGGTTGTTAATATATATTTCGA[T/G]
CTAAGTGATTTATACTGTCTCGGCAAGGCAACCGATTTATCCCAATCACTTGATTTAAATTTATATCGATATAAGGATTATATGTTGTTAACAACTGTAG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 54.90% 44.30% 0.30% 0.53% NA
All Indica  2759 29.40% 69.20% 0.51% 0.83% NA
All Japonica  1512 89.80% 10.10% 0.00% 0.07% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 7.40% 91.90% 0.34% 0.34% NA
Indica II  465 37.00% 62.20% 0.00% 0.86% NA
Indica III  913 33.40% 64.20% 1.10% 1.31% NA
Indica Intermediate  786 37.00% 62.10% 0.25% 0.64% NA
Temperate Japonica  767 97.70% 2.30% 0.00% 0.00% NA
Tropical Japonica  504 81.00% 19.00% 0.00% 0.00% NA
Japonica Intermediate  241 83.40% 16.20% 0.00% 0.41% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 68.90% 30.00% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1012424922 A -> C LOC_Os10g24250.1 upstream_gene_variant ; 410.0bp to feature; MODIFIER silent_mutation Average:25.787; most accessible tissue: Minghui63 flag leaf, score: 38.911 N N N N
vg1012424922 A -> C LOC_Os10g24250-LOC_Os10g24260 intergenic_region ; MODIFIER silent_mutation Average:25.787; most accessible tissue: Minghui63 flag leaf, score: 38.911 N N N N
vg1012424922 A -> DEL N N silent_mutation Average:25.787; most accessible tissue: Minghui63 flag leaf, score: 38.911 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1012424922 NA 1.75E-07 mr1328 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
vg1012424922 NA 8.71E-09 mr1342 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
vg1012424922 NA 6.05E-07 mr1446 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
vg1012424922 NA 3.78E-07 mr1716 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
vg1012424922 NA 2.49E-10 mr1827 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
vg1012424922 8.43E-09 NA mr1446_2 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
vg1012424922 8.74E-08 1.35E-10 mr1446_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
vg1012424922 NA 4.73E-07 mr1668_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