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Detailed information for vg0106635826:

Variant ID: vg0106635826 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 6635826
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:


TATCATAAACATGGCTAAACTTGAAAGAACATAATTAATCAACACCAGTCTACCACCAACAGATAAATGCTTGCCTTTCCAACTACTAAGCTTTTTCTCA[A/C]
TTCTCTCTTCAATAAGTTTCCAATCTTTATTAGAAAGCTTCCTAAAATGCATTGAAATTCCAAGGTATTTAAAAGGAAAGGTACCTAACTTACAACCAAA

Reverse complement sequence

TTTGGTTGTAAGTTAGGTACCTTTCCTTTTAAATACCTTGGAATTTCAATGCATTTTAGGAAGCTTTCTAATAAAGATTGGAAACTTATTGAAGAGAGAA[T/G]
TGAGAAAAAGCTTAGTAGTTGGAAAGGCAAGCATTTATCTGTTGGTGGTAGACTGGTGTTGATTAATTATGTTCTTTCAAGTTTAGCCATGTTTATGATA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.70% 4.10% 0.15% 0.00% NA
All Indica  2759 93.00% 6.80% 0.25% 0.00% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 90.60% 8.40% 1.01% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.00% 1.00% 0.00% 0.00% NA
Indica Intermediate  786 83.70% 16.20% 0.13% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 98.80% 1.20% 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  90 100.00% 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
vg0106635826 A -> C LOC_Os01g12170.1 intron_variant ; MODIFIER silent_mutation Average:17.66; most accessible tissue: Zhenshan97 flower, score: 25.055 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0106635826 NA 3.96E-06 mr1013 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
vg0106635826 NA 1.14E-07 mr1015 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
vg0106635826 NA 8.31E-06 mr1034 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
vg0106635826 NA 6.68E-06 mr1056 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
vg0106635826 NA 8.69E-06 mr1296_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
vg0106635826 NA 4.57E-06 mr1474_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
vg0106635826 7.37E-06 7.37E-06 mr1738_2 Ind_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
vg0106635826 NA 8.45E-06 mr1825_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