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Detailed information for vg0906681211:

Variant ID: vg0906681211 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 6681211
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.01, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:


CAAATAATTATTGTAACAATTTTTAAATTTTTGTACCTCTTTTCGCAGGCAGCGAATTCTAATTTTTGCAGGCGGACGTTGCATATTTTCCTAGGCAGCC[C/T]
GTTTAGCTCCACTTCGCCTGGGAAAAAAATCTTCCCAGGCAGGCGTCCCGCCGCCGATCTTCGCAGTCGTTTGGGTGCAAGTGGAGCGTCCGGGAAGACT

Reverse complement sequence

AGTCTTCCCGGACGCTCCACTTGCACCCAAACGACTGCGAAGATCGGCGGCGGGACGCCTGCCTGGGAAGATTTTTTTCCCAGGCGAAGTGGAGCTAAAC[G/A]
GGCTGCCTAGGAAAATATGCAACGTCCGCCTGCAAAAATTAGAATTCGCTGCCTGCGAAAAGAGGTACAAAAATTTAAAAATTGTTACAATAATTATTTG

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 80.20% 13.20% 5.23% 1.40% NA
All Indica  2759 77.20% 12.10% 8.48% 2.28% NA
All Japonica  1512 83.50% 16.00% 0.33% 0.20% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 87.90% 2.40% 8.07% 1.68% NA
Indica II  465 63.70% 28.80% 6.67% 0.86% NA
Indica III  913 83.00% 5.90% 8.00% 3.07% NA
Indica Intermediate  786 70.20% 16.70% 10.43% 2.67% NA
Temperate Japonica  767 84.10% 15.90% 0.00% 0.00% NA
Tropical Japonica  504 88.90% 10.90% 0.20% 0.00% NA
Japonica Intermediate  241 70.10% 27.00% 1.66% 1.24% NA
VI/Aromatic  96 67.70% 30.20% 2.08% 0.00% NA
Intermediate  90 73.30% 20.00% 6.67% 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
vg0906681211 C -> DEL N N silent_mutation Average:39.651; most accessible tissue: Callus, score: 62.689 N N N N
vg0906681211 C -> T LOC_Os09g11890.1 downstream_gene_variant ; 2236.0bp to feature; MODIFIER silent_mutation Average:39.651; most accessible tissue: Callus, score: 62.689 N N N N
vg0906681211 C -> T LOC_Os09g11890-LOC_Os09g11900 intergenic_region ; MODIFIER silent_mutation Average:39.651; most accessible tissue: Callus, score: 62.689 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0906681211 NA 9.37E-06 mr1245 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
vg0906681211 NA 5.77E-06 mr1280 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
vg0906681211 NA 6.65E-06 mr1280 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
vg0906681211 NA 3.67E-06 mr1318 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
vg0906681211 NA 7.21E-07 mr1788 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
vg0906681211 NA 4.47E-06 mr1974 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
vg0906681211 NA 3.62E-06 mr1063_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
vg0906681211 7.21E-06 7.21E-06 mr1141_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
vg0906681211 NA 3.84E-07 mr1298_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
vg0906681211 NA 1.30E-07 mr1318_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
vg0906681211 NA 7.10E-07 mr1510_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
vg0906681211 NA 7.51E-06 mr1531_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
vg0906681211 2.77E-06 2.77E-06 mr1574_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
vg0906681211 NA 8.02E-06 mr1617_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
vg0906681211 9.69E-06 3.00E-08 mr1702_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
vg0906681211 NA 6.80E-07 mr1729_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
vg0906681211 NA 1.00E-06 mr1731_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
vg0906681211 NA 1.77E-09 mr1788_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
vg0906681211 NA 1.29E-06 mr1996_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