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Detailed information for vg1217438475:

Variant ID: vg1217438475 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 17438475
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.76, T: 0.24, others allele: 0.00, population size: 182. )

Flanking Sequence (100 bp) in Reference Genome:


TATATTGGTGGGAGCTTCTGCAATATGTTGGGCTCTGTGGTTGAGTAGGAATGATATGGTTTGACAAATCACCATCTATTTCTTATATGTAGGTAATTTT[C/T]
AGGGCAACATATTAGCTCCGGTTTTGGGCACAACTACAAAGGTGTGATGAATACAAAGGTGTGATGAAGACGGTGAGTTTTTAAAAGTTGTATGTCGTAA

Reverse complement sequence

TTACGACATACAACTTTTAAAAACTCACCGTCTTCATCACACCTTTGTATTCATCACACCTTTGTAGTTGTGCCCAAAACCGGAGCTAATATGTTGCCCT[G/A]
AAAATTACCTACATATAAGAAATAGATGGTGATTTGTCAAACCATATCATTCCTACTCAACCACAGAGCCCAACATATTGCAGAAGCTCCCACCAATATA

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 59.90% 40.00% 0.06% 0.00% NA
All Indica  2759 86.70% 13.20% 0.11% 0.00% NA
All Japonica  1512 22.10% 77.90% 0.00% 0.00% NA
Aus  269 20.10% 79.90% 0.00% 0.00% NA
Indica I  595 88.70% 10.90% 0.34% 0.00% NA
Indica II  465 82.80% 17.20% 0.00% 0.00% NA
Indica III  913 88.80% 11.20% 0.00% 0.00% NA
Indica Intermediate  786 84.90% 15.00% 0.13% 0.00% NA
Temperate Japonica  767 5.90% 94.10% 0.00% 0.00% NA
Tropical Japonica  504 41.50% 58.50% 0.00% 0.00% NA
Japonica Intermediate  241 33.20% 66.80% 0.00% 0.00% NA
VI/Aromatic  96 14.60% 85.40% 0.00% 0.00% NA
Intermediate  90 43.30% 56.70% 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
vg1217438475 C -> T LOC_Os12g29370.1 upstream_gene_variant ; 3074.0bp to feature; MODIFIER silent_mutation Average:35.049; most accessible tissue: Zhenshan97 young leaf, score: 65.804 N N N N
vg1217438475 C -> T LOC_Os12g29360-LOC_Os12g29370 intergenic_region ; MODIFIER silent_mutation Average:35.049; most accessible tissue: Zhenshan97 young leaf, score: 65.804 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1217438475 NA 5.42E-07 mr1168 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
vg1217438475 NA 2.21E-08 mr1383 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
vg1217438475 NA 8.92E-06 mr1388 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
vg1217438475 NA 1.46E-08 mr1624 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