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Detailed information for vg1207114214:

Variant ID: vg1207114214 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 7114214
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: 345. )

Flanking Sequence (100 bp) in Reference Genome:


CCTCTCAGTGTGCTTCAAACCTGGTACAAAATATAGCTATTTCATATAGTTCAATCCACATATACCATATATCAACAAATATTTAAGTATCGATCATGCA[C/T]
GATTCTTCCCCATTAGGTGCAAGATTCAATGAGATTGTTGGATCTCCCTACTACATGGCACCAGAAGTCCTGAAGAGAAACTATGGACAAGAAATAGACA

Reverse complement sequence

TGTCTATTTCTTGTCCATAGTTTCTCTTCAGGACTTCTGGTGCCATGTAGTAGGGAGATCCAACAATCTCATTGAATCTTGCACCTAATGGGGAAGAATC[G/A]
TGCATGATCGATACTTAAATATTTGTTGATATATGGTATATGTGGATTGAACTATATGAAATAGCTATATTTTGTACCAGGTTTGAAGCACACTGAGAGG

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 80.90% 19.10% 0.02% 0.00% NA
All Indica  2759 68.00% 32.00% 0.04% 0.00% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 48.60% 51.40% 0.00% 0.00% NA
Indica II  465 44.70% 55.30% 0.00% 0.00% NA
Indica III  913 93.90% 6.00% 0.11% 0.00% NA
Indica Intermediate  786 66.40% 33.60% 0.00% 0.00% NA
Temperate Japonica  767 99.10% 0.90% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 88.90% 11.10% 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
vg1207114214 C -> T LOC_Os12g12860.1 intron_variant ; MODIFIER silent_mutation Average:57.147; most accessible tissue: Callus, score: 87.544 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1207114214 NA 6.53E-06 mr1177 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
vg1207114214 NA 7.18E-07 mr1177 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
vg1207114214 NA 2.80E-06 mr1002_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
vg1207114214 6.44E-07 4.81E-10 mr1024_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
vg1207114214 NA 5.78E-09 mr1220_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
vg1207114214 NA 2.62E-17 mr1352_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
vg1207114214 NA 3.92E-07 mr1378_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
vg1207114214 NA 8.07E-06 mr1428_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
vg1207114214 NA 2.72E-09 mr1627_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
vg1207114214 NA 1.78E-07 mr1864_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