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Detailed information for vg1015794903:

Variant ID: vg1015794903 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 15794903
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 300. )

Flanking Sequence (100 bp) in Reference Genome:


GAAAACCTTCCGATTTGCCCACGAGACGGGTAGTTATCCTCATATCGATCTAAATTGGCCTAGAGGCTGATTTTGATCTCTAAATCGGCTCCGCTAGCCG[G/C]
TTTAGTTTTTCTTTTTGCAAAACCCATCTTGATTTGGCCTTTTGGCTAGATCGAGGTGGTTGACGACTCCATATCACCGCAAGGCGTTTCGGTGCTGCGA

Reverse complement sequence

TCGCAGCACCGAAACGCCTTGCGGTGATATGGAGTCGTCAACCACCTCGATCTAGCCAAAAGGCCAAATCAAGATGGGTTTTGCAAAAAGAAAAACTAAA[C/G]
CGGCTAGCGGAGCCGATTTAGAGATCAAAATCAGCCTCTAGGCCAATTTAGATCGATATGAGGATAACTACCCGTCTCGTGGGCAAATCGGAAGGTTTTC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.10% 2.10% 0.83% 0.00% NA
All Indica  2759 95.20% 3.40% 1.38% 0.00% NA
All Japonica  1512 99.70% 0.20% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 85.70% 10.30% 4.03% 0.00% NA
Indica II  465 96.60% 2.80% 0.65% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 95.90% 2.70% 1.40% 0.00% NA
Temperate Japonica  767 99.70% 0.10% 0.13% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 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
vg1015794903 G -> C LOC_Os10g30380.1 upstream_gene_variant ; 2436.0bp to feature; MODIFIER silent_mutation Average:34.673; most accessible tissue: Zhenshan97 flower, score: 69.089 N N N N
vg1015794903 G -> C LOC_Os10g30390.1 downstream_gene_variant ; 1275.0bp to feature; MODIFIER silent_mutation Average:34.673; most accessible tissue: Zhenshan97 flower, score: 69.089 N N N N
vg1015794903 G -> C LOC_Os10g30380-LOC_Os10g30390 intergenic_region ; MODIFIER silent_mutation Average:34.673; most accessible tissue: Zhenshan97 flower, score: 69.089 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1015794903 2.49E-06 NA mr1005 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