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Detailed information for vg0705766254:

Variant ID: vg0705766254 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 5766254
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 327. )

Flanking Sequence (100 bp) in Reference Genome:


TATGTTCCTTCAATGCTTCAAACCTGTTCCCCTTAAGTATCTCTTCAGCACTGCCCTCATCTATTATGTCACTCCCACTCCTCCATTGCTTATTATACCA[C/T]
TCCCACTCTTCCATTGTAGGGTTAGTCTGATAACAATTTGGTCTCATGTGCTTCAGTTAACCTCCACTCTGTATCGTCCATTCTACAACTCCTCCTGCCC

Reverse complement sequence

GGGCAGGAGGAGTTGTAGAATGGACGATACAGAGTGGAGGTTAACTGAAGCACATGAGACCAAATTGTTATCAGACTAACCCTACAATGGAAGAGTGGGA[G/A]
TGGTATAATAAGCAATGGAGGAGTGGGAGTGACATAATAGATGAGGGCAGTGCTGAAGAGATACTTAAGGGGAACAGGTTTGAAGCATTGAAGGAACATA

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 98.40% 1.00% 0.63% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 95.30% 2.80% 1.92% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 91.30% 5.30% 3.39% 0.00% NA
Tropical Japonica  504 99.60% 0.20% 0.20% 0.00% NA
Japonica Intermediate  241 99.20% 0.00% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 2.20% 1.11% 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
vg0705766254 C -> T LOC_Os07g10610.2 3_prime_UTR_variant ; 1508.0bp to feature; MODIFIER silent_mutation Average:68.868; most accessible tissue: Callus, score: 81.153 N N N N
vg0705766254 C -> T LOC_Os07g10620.1 upstream_gene_variant ; 3295.0bp to feature; MODIFIER silent_mutation Average:68.868; most accessible tissue: Callus, score: 81.153 N N N N
vg0705766254 C -> T LOC_Os07g10610.1 intron_variant ; MODIFIER silent_mutation Average:68.868; most accessible tissue: Callus, score: 81.153 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0705766254 NA 7.40E-07 mr1028 Jap_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
vg0705766254 5.23E-07 5.23E-07 mr1369 Jap_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
vg0705766254 NA 2.44E-06 mr1453 Jap_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
vg0705766254 NA 3.04E-06 mr1648 Jap_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
vg0705766254 NA 1.64E-07 mr1652 Jap_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
vg0705766254 NA 4.60E-06 mr1697 Jap_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