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Detailed information for vg0510636377:

Variant ID: vg0510636377 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 10636377
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


GAAAAAACACTAATAAAAACCAAATAAACAGTACAATTAAAGTTCACAAATAGGTAGAGCTTGAATTCAGATGAATTATGAGACTTGAACGACCTCATTC[C/T]
GAGTTCGTATGAATTAGATATGAATTTTACAAGATTTAATTCCAATTAAACCTATTAAAGAAAAGACTATTCCAAATTGATTAAACAATTTACAAATGAC

Reverse complement sequence

GTCATTTGTAAATTGTTTAATCAATTTGGAATAGTCTTTTCTTTAATAGGTTTAATTGGAATTAAATCTTGTAAAATTCATATCTAATTCATACGAACTC[G/A]
GAATGAGGTCGTTCAAGTCTCATAATTCATCTGAATTCAAGCTCTACCTATTTGTGAACTTTAATTGTACTGTTTATTTGGTTTTTATTAGTGTTTTTTC

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 90.90% 7.50% 1.61% 0.00% NA
All Indica  2759 91.00% 6.20% 2.75% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 36.10% 63.90% 0.00% 0.00% NA
Indica I  595 92.40% 0.00% 7.56% 0.00% NA
Indica II  465 99.10% 0.40% 0.43% 0.00% NA
Indica III  913 83.00% 15.40% 1.53% 0.00% NA
Indica Intermediate  786 94.40% 3.70% 1.91% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg0510636377 C -> T LOC_Os05g18400.1 downstream_gene_variant ; 1351.0bp to feature; MODIFIER silent_mutation Average:18.817; most accessible tissue: Zhenshan97 panicle, score: 28.447 N N N N
vg0510636377 C -> T LOC_Os05g18390-LOC_Os05g18400 intergenic_region ; MODIFIER silent_mutation Average:18.817; most accessible tissue: Zhenshan97 panicle, score: 28.447 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0510636377 NA 7.11E-06 mr1230 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
vg0510636377 4.96E-06 NA mr1304_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
vg0510636377 6.16E-06 NA mr1386_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