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Detailed information for vg0624941329:

Variant ID: vg0624941329 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 24941329
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:


AGGTTTCTCAGGCTCCTCAGTGATACTAGTCCGTAGCAGGACTCTATAAGCACCTTTGTTAATGTTGTCAGGTTGCCATTATCAGGTAGTTCCTTCAATT[T/C]
GGGGCAATCCCTTATGATCAAATTCTGGAGGGCAGGAAAACACCCAAAGTCCACCAATGATGTTACATTGGGGCAATCTACAATTTCCATTTCATTTAAC

Reverse complement sequence

GTTAAATGAAATGGAAATTGTAGATTGCCCCAATGTAACATCATTGGTGGACTTTGGGTGTTTTCCTGCCCTCCAGAATTTGATCATAAGGGATTGCCCC[A/G]
AATTGAAGGAACTACCTGATAATGGCAACCTGACAACATTAACAAAGGTGCTTATAGAGTCCTGCTACGGACTAGTATCACTGAGGAGCCTGAGAAACCT

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 56.90% 0.00% 0.17% 42.93% NA
All Indica  2759 29.00% 0.10% 0.25% 70.71% NA
All Japonica  1512 99.20% 0.00% 0.00% 0.79% NA
Aus  269 87.00% 0.00% 0.00% 13.01% NA
Indica I  595 67.40% 0.00% 0.00% 32.61% NA
Indica II  465 10.10% 0.00% 0.65% 89.25% NA
Indica III  913 13.60% 0.00% 0.00% 86.42% NA
Indica Intermediate  786 28.90% 0.30% 0.51% 70.36% NA
Temperate Japonica  767 99.00% 0.00% 0.00% 1.04% NA
Tropical Japonica  504 99.20% 0.00% 0.00% 0.79% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 0.00% 0.00% 2.08% NA
Intermediate  90 66.70% 0.00% 1.11% 32.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0624941329 T -> C LOC_Os06g41660.1 missense_variant ; p.Lys1017Glu; MODERATE nonsynonymous_codon ; K1017E Average:38.295; most accessible tissue: Zhenshan97 root, score: 62.394 benign -1.068 TOLERATED 1.00
vg0624941329 T -> DEL LOC_Os06g41660.1 N frameshift_variant Average:38.295; most accessible tissue: Zhenshan97 root, score: 62.394 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0624941329 2.07E-06 1.57E-07 mr1974_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
vg0624941329 7.56E-06 4.99E-06 mr1974_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