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Detailed information for vg0222623248:

Variant ID: vg0222623248 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 22623248
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:


GTACTTCTAATACCACTAGCTACTAAAAATGCATATAAAGATCGACGCTATAGGGTACCAAAACAGCTAAAACTAACACCTATAGTGCGTTTCTCTCCTT[C/T]
ACGAGTTAAGAACACATAAAACAGGCATCTATACATGTGCAAGGTTTCTGGTGTAGTAGGACTCGTACTGTGCGCAAGACGATGTGCTGGGGAGAAACAG

Reverse complement sequence

CTGTTTCTCCCCAGCACATCGTCTTGCGCACAGTACGAGTCCTACTACACCAGAAACCTTGCACATGTATAGATGCCTGTTTTATGTGTTCTTAACTCGT[G/A]
AAGGAGAGAAACGCACTATAGGTGTTAGTTTTAGCTGTTTTGGTACCCTATAGCGTCGATCTTTATATGCATTTTTAGTAGCTAGTGGTATTAGAAGTAC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.90% 6.10% 0.00% 0.00% NA
All Indica  2759 96.10% 3.90% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 37.90% 62.10% 0.00% 0.00% NA
Indica I  595 99.00% 1.00% 0.00% 0.00% NA
Indica II  465 94.80% 5.20% 0.00% 0.00% NA
Indica III  913 98.20% 1.80% 0.00% 0.00% NA
Indica Intermediate  786 92.10% 7.90% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 90.60% 9.40% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0222623248 C -> T LOC_Os02g37490.1 upstream_gene_variant ; 3024.0bp to feature; MODIFIER silent_mutation Average:71.204; most accessible tissue: Callus, score: 96.086 N N N N
vg0222623248 C -> T LOC_Os02g37470.1 downstream_gene_variant ; 3143.0bp to feature; MODIFIER silent_mutation Average:71.204; most accessible tissue: Callus, score: 96.086 N N N N
vg0222623248 C -> T LOC_Os02g37480.1 downstream_gene_variant ; 60.0bp to feature; MODIFIER silent_mutation Average:71.204; most accessible tissue: Callus, score: 96.086 N N N N
vg0222623248 C -> T LOC_Os02g37480-LOC_Os02g37490 intergenic_region ; MODIFIER silent_mutation Average:71.204; most accessible tissue: Callus, score: 96.086 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0222623248 8.52E-06 NA mr1069 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
vg0222623248 7.18E-06 NA mr1099 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
vg0222623248 9.84E-08 NA mr1101 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
vg0222623248 NA 3.00E-14 mr1496 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
vg0222623248 8.83E-06 NA mr1962 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
vg0222623248 7.84E-08 NA mr1098_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
vg0222623248 1.26E-07 NA mr1099_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
vg0222623248 4.89E-06 NA mr1123_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
vg0222623248 2.71E-08 NA mr1150_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
vg0222623248 5.51E-06 1.12E-17 mr1240_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
vg0222623248 NA 8.74E-07 mr1378_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
vg0222623248 7.34E-06 NA mr1495_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
vg0222623248 NA 2.67E-13 mr1496_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
vg0222623248 NA 3.21E-08 mr1968_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