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Detailed information for vg1000205246:

Variant ID: vg1000205246 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 205246
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.74, T: 0.27, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:


CCACAGTTTCTTTGCCTTTATTTCTTGTTGATTACAGGATCAAATCAACTGGCACGCTAGTACACCCGAATGCGAGCTTTGGACCTGCACTGGAGTTAAG[T/C]
AGATCTCCTAGGCCTCGTGTTTTCTGTCAACACCATGCGACCTAGGACAGGCTGGGGTTCAGTACCTCCTGCTTCTCTTTCCATGGTCCCACGACCGGGA

Reverse complement sequence

TCCCGGTCGTGGGACCATGGAAAGAGAAGCAGGAGGTACTGAACCCCAGCCTGTCCTAGGTCGCATGGTGTTGACAGAAAACACGAGGCCTAGGAGATCT[A/G]
CTTAACTCCAGTGCAGGTCCAAAGCTCGCATTCGGGTGTACTAGCGTGCCAGTTGATTTGATCCTGTAATCAACAAGAAATAAAGGCAAAGAAACTGTGG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 19.70% 17.80% 0.59% 61.85% NA
All Indica  2759 2.50% 28.50% 0.76% 68.21% NA
All Japonica  1512 54.20% 1.60% 0.20% 43.98% NA
Aus  269 4.80% 4.80% 0.37% 89.96% NA
Indica I  595 2.20% 18.50% 1.01% 78.32% NA
Indica II  465 3.40% 46.00% 0.65% 49.89% NA
Indica III  913 2.30% 23.20% 0.55% 73.93% NA
Indica Intermediate  786 2.40% 31.90% 0.89% 64.76% NA
Temperate Japonica  767 85.50% 1.00% 0.26% 13.17% NA
Tropical Japonica  504 8.70% 2.20% 0.20% 88.89% NA
Japonica Intermediate  241 49.80% 2.10% 0.00% 48.13% NA
VI/Aromatic  96 10.40% 1.00% 0.00% 88.54% NA
Intermediate  90 23.30% 18.90% 3.33% 54.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1000205246 T -> C LOC_Os10g01330.1 upstream_gene_variant ; 2222.0bp to feature; MODIFIER silent_mutation Average:23.776; most accessible tissue: Zhenshan97 flag leaf, score: 58.772 N N N N
vg1000205246 T -> C LOC_Os10g01340.1 downstream_gene_variant ; 3627.0bp to feature; MODIFIER silent_mutation Average:23.776; most accessible tissue: Zhenshan97 flag leaf, score: 58.772 N N N N
vg1000205246 T -> C LOC_Os10g01330-LOC_Os10g01340 intergenic_region ; MODIFIER silent_mutation Average:23.776; most accessible tissue: Zhenshan97 flag leaf, score: 58.772 N N N N
vg1000205246 T -> DEL N N silent_mutation Average:23.776; most accessible tissue: Zhenshan97 flag leaf, score: 58.772 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1000205246 NA 1.10E-21 mr1300 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
vg1000205246 NA 5.28E-45 mr1563 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
vg1000205246 2.79E-08 5.17E-40 mr1926 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
vg1000205246 1.17E-07 NA mr1113_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
vg1000205246 1.15E-06 NA mr1114_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
vg1000205246 2.06E-06 NA mr1117_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
vg1000205246 4.59E-06 NA mr1119_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
vg1000205246 1.45E-07 NA mr1120_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
vg1000205246 7.15E-06 NA mr1123_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
vg1000205246 1.58E-09 NA mr1247_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
vg1000205246 NA 3.91E-08 mr1299_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
vg1000205246 NA 4.20E-07 mr1727_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
vg1000205246 NA 4.85E-06 mr1785_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
vg1000205246 NA 1.95E-09 mr1947_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