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Detailed information for vg1013490779:

Variant ID: vg1013490779 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 13490779
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: 268. )

Flanking Sequence (100 bp) in Reference Genome:


AATCCAATCATCTCCAAAACCACTTCGTAAATAAATTCCAAATAACAAAACCAGTAATCTCCAATGCCCAATTGTTCATCACAGAATAATAATAAAAAAA[C/T]
ACCTTTGATTTTACATAAACGACTTAGGCCCTGTTTAGTTCCCAAACAAAAATTTTTCACCCTATCACATTAAATATTTGGACATATTCATGGAGTATTA

Reverse complement sequence

TAATACTCCATGAATATGTCCAAATATTTAATGTGATAGGGTGAAAAATTTTTGTTTGGGAACTAAACAGGGCCTAAGTCGTTTATGTAAAATCAAAGGT[G/A]
TTTTTTTATTATTATTCTGTGATGAACAATTGGGCATTGGAGATTACTGGTTTTGTTATTTGGAATTTATTTACGAAGTGGTTTTGGAGATGATTGGATT

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% 1.80% 0.95% 0.00% NA
All Indica  2759 95.30% 3.10% 1.59% 0.00% NA
All Japonica  1512 99.90% 0.00% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 88.90% 6.60% 4.54% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 92.60% 5.20% 2.16% 0.00% NA
Temperate Japonica  767 99.90% 0.00% 0.13% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 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
vg1013490779 C -> T LOC_Os10g26040.1 upstream_gene_variant ; 536.0bp to feature; MODIFIER silent_mutation Average:44.511; most accessible tissue: Zhenshan97 panicle, score: 73.605 N N N N
vg1013490779 C -> T LOC_Os10g26050.1 upstream_gene_variant ; 2005.0bp to feature; MODIFIER silent_mutation Average:44.511; most accessible tissue: Zhenshan97 panicle, score: 73.605 N N N N
vg1013490779 C -> T LOC_Os10g26050.2 upstream_gene_variant ; 2005.0bp to feature; MODIFIER silent_mutation Average:44.511; most accessible tissue: Zhenshan97 panicle, score: 73.605 N N N N
vg1013490779 C -> T LOC_Os10g26050.3 upstream_gene_variant ; 2005.0bp to feature; MODIFIER silent_mutation Average:44.511; most accessible tissue: Zhenshan97 panicle, score: 73.605 N N N N
vg1013490779 C -> T LOC_Os10g26050.4 upstream_gene_variant ; 2006.0bp to feature; MODIFIER silent_mutation Average:44.511; most accessible tissue: Zhenshan97 panicle, score: 73.605 N N N N
vg1013490779 C -> T LOC_Os10g26040-LOC_Os10g26050 intergenic_region ; MODIFIER silent_mutation Average:44.511; most accessible tissue: Zhenshan97 panicle, score: 73.605 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1013490779 1.06E-08 1.90E-09 mr1533 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
vg1013490779 9.06E-11 1.20E-11 mr1980 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
vg1013490779 NA 1.04E-06 mr1533_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
vg1013490779 4.40E-06 4.40E-06 mr1982_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