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Detailed information for vg0726195894:

Variant ID: vg0726195894 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 26195894
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: 272. )

Flanking Sequence (100 bp) in Reference Genome:


GACAAGGCATTTCGAAAGCCGACACAGGTTCACCATATGCCAACGAGAGGGGTCCCAGACCGACATCAGGTTAGGTCCCAGACCATACTGTGCCAGGAAG[C/T]
CCGGGGGTTCTCCCCGGCACTACCCCGTTGAATCCACATGTCTCTTGGCATCATGGTTCCCCCGATAATCTAATTACTCAGCCAGGGGTGTCCCATTCCA

Reverse complement sequence

TGGAATGGGACACCCCTGGCTGAGTAATTAGATTATCGGGGGAACCATGATGCCAAGAGACATGTGGATTCAACGGGGTAGTGCCGGGGAGAACCCCCGG[G/A]
CTTCCTGGCACAGTATGGTCTGGGACCTAACCTGATGTCGGTCTGGGACCCCTCTCGTTGGCATATGGTGAACCTGTGTCGGCTTTCGAAATGCCTTGTC

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% 9.00% 0.11% 0.00% NA
All Indica  2759 86.50% 13.30% 0.18% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 79.20% 20.80% 0.00% 0.00% NA
Indica I  595 96.60% 3.20% 0.17% 0.00% NA
Indica II  465 93.80% 6.00% 0.22% 0.00% NA
Indica III  913 77.20% 22.70% 0.11% 0.00% NA
Indica Intermediate  786 85.20% 14.50% 0.25% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0726195894 C -> T LOC_Os07g43780.1 downstream_gene_variant ; 2015.0bp to feature; MODIFIER silent_mutation Average:53.255; most accessible tissue: Zhenshan97 flag leaf, score: 74.825 N N N N
vg0726195894 C -> T LOC_Os07g43790.1 downstream_gene_variant ; 3828.0bp to feature; MODIFIER silent_mutation Average:53.255; most accessible tissue: Zhenshan97 flag leaf, score: 74.825 N N N N
vg0726195894 C -> T LOC_Os07g43770-LOC_Os07g43780 intergenic_region ; MODIFIER silent_mutation Average:53.255; most accessible tissue: Zhenshan97 flag leaf, score: 74.825 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0726195894 NA 5.56E-06 mr1158_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
vg0726195894 1.67E-07 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
vg0726195894 8.42E-07 NA mr1521_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
vg0726195894 7.21E-06 NA mr1934_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