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Detailed information for vg1206433446:

Variant ID: vg1206433446 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 6433446
Reference Allele: TAlternative Allele: G
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.70, T: 0.30, others allele: 0.00, population size: 77. )

Flanking Sequence (100 bp) in Reference Genome:


TATTGATTCGAAGATTCCAGTTGATTCGGAAGGAATTTTGATGTAGGACCAAATCCATTGGAAAGGTGGTCTCGTTAGCTTTCCATGCATATGTAGAACA[T/G]
CGAAATCGGAGTCAGAATACAACCTGGGCGATGAATTTAGTGTGTAATACTCCTGGAGCCTGAAGTGGACTTAAACTTGATATGAGTTGGATCTCCATCT

Reverse complement sequence

AGATGGAGATCCAACTCATATCAAGTTTAAGTCCACTTCAGGCTCCAGGAGTATTACACACTAAATTCATCGCCCAGGTTGTATTCTGACTCCGATTTCG[A/C]
TGTTCTACATATGCATGGAAAGCTAACGAGACCACCTTTCCAATGGATTTGGTCCTACATCAAAATTCCTTCCGAATCAACTGGAATCTTCGAATCAATA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 25.30% 16.40% 0.30% 58.04% NA
All Indica  2759 36.60% 7.80% 0.25% 55.35% NA
All Japonica  1512 5.80% 31.10% 0.33% 62.83% NA
Aus  269 1.50% 21.90% 0.37% 76.21% NA
Indica I  595 86.70% 4.20% 0.34% 8.74% NA
Indica II  465 20.60% 18.70% 0.22% 60.43% NA
Indica III  913 11.30% 3.40% 0.33% 84.99% NA
Indica Intermediate  786 37.70% 9.00% 0.13% 53.18% NA
Temperate Japonica  767 8.90% 40.70% 0.65% 49.80% NA
Tropical Japonica  504 2.40% 10.70% 0.00% 86.90% NA
Japonica Intermediate  241 2.90% 43.20% 0.00% 53.94% NA
VI/Aromatic  96 69.80% 10.40% 0.00% 19.79% NA
Intermediate  90 30.00% 22.20% 1.11% 46.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1206433446 T -> DEL N N silent_mutation Average:57.738; most accessible tissue: Minghui63 flag leaf, score: 75.722 N N N N
vg1206433446 T -> G LOC_Os12g11840.1 downstream_gene_variant ; 3654.0bp to feature; MODIFIER silent_mutation Average:57.738; most accessible tissue: Minghui63 flag leaf, score: 75.722 N N N N
vg1206433446 T -> G LOC_Os12g11840-LOC_Os12g11860 intergenic_region ; MODIFIER silent_mutation Average:57.738; most accessible tissue: Minghui63 flag leaf, score: 75.722 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1206433446 7.58E-07 7.58E-07 mr1173 Jap_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
vg1206433446 3.35E-08 3.35E-08 mr1381 Jap_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
vg1206433446 NA 2.83E-08 mr1030_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
vg1206433446 NA 9.07E-06 mr1278_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
vg1206433446 NA 4.99E-06 mr1329_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
vg1206433446 NA 3.85E-07 mr1524_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
vg1206433446 4.96E-07 NA mr1549_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
vg1206433446 NA 4.07E-08 mr1683_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
vg1206433446 NA 2.78E-06 mr1687_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
vg1206433446 NA 7.80E-08 mr1749_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
vg1206433446 NA 1.80E-08 mr1821_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
vg1206433446 1.53E-06 3.10E-07 mr1923_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