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Detailed information for vg0210828426:

Variant ID: vg0210828426 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 10828426
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: 281. )

Flanking Sequence (100 bp) in Reference Genome:


GAAGCTCCCTATGACCCCGTACTTAACGATGATCTCCCATGATGGACAGAACGACTACGGGAATCAGTAGCCAATCTCAGTAACGCGTTCGAGGAGGTCG[C/T]
TACCAGAGCACAACCAGAACATCTGACGGTTGGCGGTGCCGACGGCGAACCACCGGAGCAACGGACGTCGCCTAGACGAGCTACCCCTCCACCTCGCGGC

Reverse complement sequence

GCCGCGAGGTGGAGGGGTAGCTCGTCTAGGCGACGTCCGTTGCTCCGGTGGTTCGCCGTCGGCACCGCCAACCGTCAGATGTTCTGGTTGTGCTCTGGTA[G/A]
CGACCTCCTCGAACGCGTTACTGAGATTGGCTACTGATTCCCGTAGTCGTTCTGTCCATCATGGGAGATCATCGTTAAGTACGGGGTCATAGGGAGCTTC

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 97.20% 1.90% 0.89% 0.00% NA
All Indica  2759 99.80% 0.00% 0.22% 0.00% NA
All Japonica  1512 91.60% 6.00% 2.38% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.50% 0.00% 0.50% 0.00% NA
Indica II  465 99.80% 0.00% 0.22% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.00% 0.25% 0.00% NA
Temperate Japonica  767 86.80% 8.70% 4.43% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 89.60% 10.00% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0210828426 C -> T LOC_Os02g18550.1 upstream_gene_variant ; 2699.0bp to feature; MODIFIER silent_mutation Average:70.079; most accessible tissue: Zhenshan97 flag leaf, score: 79.247 N N N N
vg0210828426 C -> T LOC_Os02g18570.1 downstream_gene_variant ; 3454.0bp to feature; MODIFIER silent_mutation Average:70.079; most accessible tissue: Zhenshan97 flag leaf, score: 79.247 N N N N
vg0210828426 C -> T LOC_Os02g18560.1 intron_variant ; MODIFIER silent_mutation Average:70.079; most accessible tissue: Zhenshan97 flag leaf, score: 79.247 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0210828426 NA 7.43E-06 mr1305_2 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
vg0210828426 6.16E-08 6.16E-08 mr1317_2 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
vg0210828426 2.52E-08 2.52E-08 mr1897_2 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
vg0210828426 1.37E-07 1.37E-07 mr1914_2 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