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Detailed information for vg0528707739:

Variant ID: vg0528707739 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 28707739
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 93. )

Flanking Sequence (100 bp) in Reference Genome:


TACAGCTAGTGTTGGCCATGGCACATAGTCGTCGCCGGTGAGCTCCTCCGGCTCATGGAGGAGGAAGAAGTGGAGCCAAGGGTAATATCATCCAGGATGG[C/T]
ATTTCGGCGAAGCCGTCTTCGTTGAACGTGGTATTTTACTGAAACTGTTTTAAGGATAGCATTCTAGTGAAGTCATTCTTTTGCAATGGTACATATGCAA

Reverse complement sequence

TTGCATATGTACCATTGCAAAAGAATGACTTCACTAGAATGCTATCCTTAAAACAGTTTCAGTAAAATACCACGTTCAACGAAGACGGCTTCGCCGAAAT[G/A]
CCATCCTGGATGATATTACCCTTGGCTCCACTTCTTCCTCCTCCATGAGCCGGAGGAGCTCACCGGCGACGACTATGTGCCATGGCCAACACTAGCTGTA

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 82.20% 13.10% 4.44% 0.23% NA
All Indica  2759 71.30% 22.20% 6.56% 0.00% NA
All Japonica  1512 97.40% 0.10% 1.85% 0.73% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 31.60% 45.00% 23.36% 0.00% NA
Indica II  465 86.20% 11.40% 2.37% 0.00% NA
Indica III  913 85.40% 14.00% 0.55% 0.00% NA
Indica Intermediate  786 76.00% 20.70% 3.31% 0.00% NA
Temperate Japonica  767 99.60% 0.10% 0.00% 0.26% NA
Tropical Japonica  504 93.30% 0.00% 5.36% 1.39% NA
Japonica Intermediate  241 98.80% 0.00% 0.41% 0.83% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 5.60% 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
vg0528707739 C -> T LOC_Os05g50080.1 downstream_gene_variant ; 3232.0bp to feature; MODIFIER silent_mutation Average:63.444; most accessible tissue: Callus, score: 93.07 N N N N
vg0528707739 C -> T LOC_Os05g50100.1 downstream_gene_variant ; 2581.0bp to feature; MODIFIER silent_mutation Average:63.444; most accessible tissue: Callus, score: 93.07 N N N N
vg0528707739 C -> T LOC_Os05g50090.1 intron_variant ; MODIFIER silent_mutation Average:63.444; most accessible tissue: Callus, score: 93.07 N N N N
vg0528707739 C -> DEL N N silent_mutation Average:63.444; most accessible tissue: Callus, score: 93.07 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0528707739 2.26E-09 1.08E-38 mr1026 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
vg0528707739 1.07E-08 5.32E-23 mr1026 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
vg0528707739 NA 7.65E-12 mr1118 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
vg0528707739 NA 9.21E-06 mr1120 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
vg0528707739 9.13E-08 3.18E-34 mr1161 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
vg0528707739 2.04E-07 5.62E-20 mr1161 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
vg0528707739 NA 5.31E-06 mr1261 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
vg0528707739 NA 2.63E-14 mr1495 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
vg0528707739 NA 5.61E-06 mr1496 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
vg0528707739 NA 3.05E-06 mr1870 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
vg0528707739 NA 8.69E-17 mr1118_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
vg0528707739 NA 8.30E-17 mr1118_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
vg0528707739 NA 1.41E-17 mr1161_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
vg0528707739 NA 2.44E-24 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
vg0528707739 NA 1.15E-18 mr1495_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
vg0528707739 NA 1.10E-06 mr1496_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
vg0528707739 NA 3.34E-06 mr1870_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
vg0528707739 NA 3.08E-08 mr1936_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