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Detailed information for vg0501804785:

Variant ID: vg0501804785 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 1804785
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.85, T: 0.15, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


ATATGACATATATTTAGTGTAAAAGTTGAAATTTATAACGTAATTATAGTGTAAACGTATTTATTTAAACTTTTTCTTGGAAAATATGCACCATAAATAT[A/T]
GTTAGTCTTTTTCTAACCAGTTTTGCTGAAAACATGTGCCATATTTTTAGTTGATTACGGTCACTTATTTCTCAGCACCGAATCTAGTATGTGGAAAAAG

Reverse complement sequence

CTTTTTCCACATACTAGATTCGGTGCTGAGAAATAAGTGACCGTAATCAACTAAAAATATGGCACATGTTTTCAGCAAAACTGGTTAGAAAAAGACTAAC[T/A]
ATATTTATGGTGCATATTTTCCAAGAAAAAGTTTAAATAAATACGTTTACACTATAATTACGTTATAAATTTCAACTTTTACACTAAATATATGTCATAT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 58.70% 41.10% 0.15% 0.00% NA
All Indica  2759 33.10% 66.90% 0.07% 0.00% NA
All Japonica  1512 97.10% 2.60% 0.33% 0.00% NA
Aus  269 90.00% 10.00% 0.00% 0.00% NA
Indica I  595 2.00% 98.00% 0.00% 0.00% NA
Indica II  465 31.60% 68.40% 0.00% 0.00% NA
Indica III  913 55.30% 44.60% 0.11% 0.00% NA
Indica Intermediate  786 31.60% 68.30% 0.13% 0.00% NA
Temperate Japonica  767 98.20% 1.70% 0.13% 0.00% NA
Tropical Japonica  504 95.60% 4.20% 0.20% 0.00% NA
Japonica Intermediate  241 96.70% 2.10% 1.24% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 67.80% 32.20% 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
vg0501804785 A -> T LOC_Os05g04010.1 upstream_gene_variant ; 4610.0bp to feature; MODIFIER silent_mutation Average:21.177; most accessible tissue: Callus, score: 61.805 N N N N
vg0501804785 A -> T LOC_Os05g04020.1 intron_variant ; MODIFIER silent_mutation Average:21.177; most accessible tissue: Callus, score: 61.805 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0501804785 NA 1.50E-15 mr1807 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
vg0501804785 2.89E-06 1.47E-07 mr1030_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
vg0501804785 4.85E-06 4.44E-06 mr1030_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
vg0501804785 NA 4.99E-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
vg0501804785 NA 5.77E-07 mr1358_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
vg0501804785 NA 1.15E-08 mr1446_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
vg0501804785 NA 9.93E-07 mr1527_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
vg0501804785 1.49E-06 9.37E-18 mr1578_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
vg0501804785 NA 8.13E-09 mr1754_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
vg0501804785 NA 4.20E-06 mr1754_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
vg0501804785 NA 1.18E-07 mr1819_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
vg0501804785 NA 1.64E-06 mr1910_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
vg0501804785 NA 1.43E-09 mr1946_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
vg0501804785 NA 1.43E-09 mr1948_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
vg0501804785 5.40E-06 NA mr1952_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
vg0501804785 4.80E-06 4.58E-08 mr1952_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