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Detailed information for vg1217982066:

Variant ID: vg1217982066 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 17982066
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.67, A: 0.34, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:


TTTTTGAATGGACACGGAGAATATGCACTGCAGTGATGGAGAATATGTGAAATCTTCAGTGATTTCCAAACCCAATCCAGTTACATCTTCCAATCAAGAA[A/C]
ACAAAATGCATATTACAGTCTCAAATCACTGAAGCAACAAAGAATCACAAGCTCAAACTGATGCAGTAAAATCAAAATATATCCCACGCCCAATCCAATT

Reverse complement sequence

AATTGGATTGGGCGTGGGATATATTTTGATTTTACTGCATCAGTTTGAGCTTGTGATTCTTTGTTGCTTCAGTGATTTGAGACTGTAATATGCATTTTGT[T/G]
TTCTTGATTGGAAGATGTAACTGGATTGGGTTTGGAAATCACTGAAGATTTCACATATTCTCCATCACTGCAGTGCATATTCTCCGTGTCCATTCAAAAA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 52.00% 47.90% 0.08% 0.00% NA
All Indica  2759 32.30% 67.60% 0.11% 0.00% NA
All Japonica  1512 85.10% 14.90% 0.07% 0.00% NA
Aus  269 60.20% 39.80% 0.00% 0.00% NA
Indica I  595 60.30% 39.70% 0.00% 0.00% NA
Indica II  465 9.00% 91.00% 0.00% 0.00% NA
Indica III  913 25.80% 74.20% 0.00% 0.00% NA
Indica Intermediate  786 32.20% 67.40% 0.38% 0.00% NA
Temperate Japonica  767 98.80% 1.20% 0.00% 0.00% NA
Tropical Japonica  504 74.80% 25.00% 0.20% 0.00% NA
Japonica Intermediate  241 62.70% 37.30% 0.00% 0.00% NA
VI/Aromatic  96 57.30% 42.70% 0.00% 0.00% NA
Intermediate  90 72.20% 27.80% 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
vg1217982066 A -> C LOC_Os12g30040.1 intron_variant ; MODIFIER silent_mutation Average:38.97; most accessible tissue: Callus, score: 85.037 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1217982066 NA 3.20E-13 mr1170 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
vg1217982066 NA 1.97E-07 mr1170 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
vg1217982066 NA 6.93E-06 mr1261 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
vg1217982066 NA 2.75E-06 mr1443 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
vg1217982066 NA 1.98E-07 mr1557 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
vg1217982066 NA 2.40E-06 mr1944 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
vg1217982066 NA 3.85E-10 mr1170_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
vg1217982066 NA 1.33E-06 mr1170_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
vg1217982066 2.81E-06 NA mr1458_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
vg1217982066 9.29E-06 5.44E-09 mr1458_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