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Detailed information for vg0518026034:

Variant ID: vg0518026034 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 18026034
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.07, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:


TTGAGAACGTTCCTGTTAAGGGAGCAGGAGTTAAACCGGACATACTTCTATCACCATGAATTCATCAACCATAATACCATATGGAGTACTCCATCCATCC[C/T]
AAAATATAAGCATTTTAGAATAGTGCCAAGTCAAACACTTTTAACTTTAACTATTAATAGCATAGAAATTAAAAAGATCAATCATGTAAAATTGATATTA

Reverse complement sequence

TAATATCAATTTTACATGATTGATCTTTTTAATTTCTATGCTATTAATAGTTAAAGTTAAAAGTGTTTGACTTGGCACTATTCTAAAATGCTTATATTTT[G/A]
GGATGGATGGAGTACTCCATATGGTATTATGGTTGATGAATTCATGGTGATAGAAGTATGTCCGGTTTAACTCCTGCTCCCTTAACAGGAACGTTCTCAA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 62.20% 37.40% 0.13% 0.32% NA
All Indica  2759 91.20% 8.40% 0.07% 0.29% NA
All Japonica  1512 19.00% 80.40% 0.26% 0.40% NA
Aus  269 33.10% 66.90% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 72.50% 26.20% 0.22% 1.08% NA
Indica III  913 95.00% 4.80% 0.00% 0.22% NA
Indica Intermediate  786 91.20% 8.50% 0.13% 0.13% NA
Temperate Japonica  767 12.90% 86.70% 0.26% 0.13% NA
Tropical Japonica  504 24.20% 75.20% 0.20% 0.40% NA
Japonica Intermediate  241 27.40% 71.00% 0.41% 1.24% NA
VI/Aromatic  96 5.20% 94.80% 0.00% 0.00% NA
Intermediate  90 46.70% 52.20% 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
vg0518026034 C -> T LOC_Os05g31020-LOC_Os05g31040 intergenic_region ; MODIFIER silent_mutation Average:60.699; most accessible tissue: Callus, score: 83.599 N N N N
vg0518026034 C -> DEL N N silent_mutation Average:60.699; most accessible tissue: Callus, score: 83.599 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0518026034 NA 1.11E-07 mr1044 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
vg0518026034 NA 1.37E-06 mr1044 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
vg0518026034 NA 3.88E-06 mr1069 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
vg0518026034 NA 1.34E-06 mr1077 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
vg0518026034 NA 3.65E-07 mr1162 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
vg0518026034 NA 2.46E-10 mr1195 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
vg0518026034 NA 2.75E-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
vg0518026034 NA 2.92E-06 mr1399 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
vg0518026034 NA 4.35E-06 mr1482 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
vg0518026034 NA 4.56E-08 mr1648 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
vg0518026034 NA 1.72E-07 mr1804 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
vg0518026034 4.33E-07 1.84E-13 mr1827 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
vg0518026034 NA 6.46E-06 mr1002_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