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Detailed information for vg0525881431:

Variant ID: vg0525881431 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 25881431
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, T: 0.02, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


AGCATTCGTGCTTTCAAGATGAAACTAAACCCGGAAAAGTGCATCTTCGGAGTACCGTCAGGGAAATTGCTCGGATTTATGGTATCTCAAAGAGGCATAC[A/T]
GGCCAACCCGGAGAAAATCAACGCCATTCTCAACATGAAACCGCCAAGCTCCCAAAAAGACGTCCAAAAGTTGACTGGTTGCATGGCGGCGCTCAGCCGG

Reverse complement sequence

CCGGCTGAGCGCCGCCATGCAACCAGTCAACTTTTGGACGTCTTTTTGGGAGCTTGGCGGTTTCATGTTGAGAATGGCGTTGATTTTCTCCGGGTTGGCC[T/A]
GTATGCCTCTTTGAGATACCATAAATCCGAGCAATTTCCCTGACGGTACTCCGAAGATGCACTTTTCCGGGTTTAGTTTCATCTTGAAAGCACGAATGCT

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 42.40% 0.40% 22.34% 34.83% NA
All Indica  2759 12.30% 0.60% 29.29% 57.81% NA
All Japonica  1512 99.10% 0.00% 0.46% 0.40% NA
Aus  269 6.70% 0.70% 85.50% 7.06% NA
Indica I  595 6.70% 0.30% 20.00% 72.94% NA
Indica II  465 25.20% 0.40% 21.72% 52.69% NA
Indica III  913 10.20% 0.90% 40.09% 48.85% NA
Indica Intermediate  786 11.30% 0.60% 28.24% 59.80% NA
Temperate Japonica  767 98.60% 0.00% 0.78% 0.65% NA
Tropical Japonica  504 99.60% 0.00% 0.20% 0.20% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 0.00% 1.04% 2.08% NA
Intermediate  90 61.10% 1.10% 11.11% 26.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0525881431 A -> T LOC_Os05g44470.1 missense_variant ; p.Gln158Leu; MODERATE nonsynonymous_codon ; Q158L Average:14.781; most accessible tissue: Minghui63 panicle, score: 20.733 possibly damaging 1.633 DELETERIOUS 0.00
vg0525881431 A -> DEL LOC_Os05g44470.1 N frameshift_variant Average:14.781; most accessible tissue: Minghui63 panicle, score: 20.733 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0525881431 NA 2.05E-22 mr1020 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
vg0525881431 NA 4.09E-17 mr1032 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
vg0525881431 NA 3.33E-06 mr1032 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
vg0525881431 NA 1.01E-16 mr1165 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
vg0525881431 NA 1.72E-17 mr1478 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
vg0525881431 NA 1.22E-06 mr1478 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
vg0525881431 NA 1.48E-09 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
vg0525881431 NA 3.11E-08 mr1896 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
vg0525881431 3.41E-06 NA mr1903 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
vg0525881431 NA 8.73E-22 mr1971 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
vg0525881431 NA 1.75E-21 mr1253_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
vg0525881431 NA 2.93E-22 mr1316_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
vg0525881431 NA 1.78E-06 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
vg0525881431 NA 3.23E-09 mr1478_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
vg0525881431 NA 2.73E-06 mr1611_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
vg0525881431 NA 6.04E-09 mr1828_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
vg0525881431 NA 6.09E-17 mr1938_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