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Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0612022465:

Variant ID: vg0612022465 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 12022465
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


ATTTTTAGCTAAATGGCTAACTAACATGACAGCTTTTAATCTTTTGTCAGCTGATTAAGGCATGTGTAACATGGGAGCGGTTAAGAATACATGTACTGTG[T/C]
GCCACCTTCTTGGTGATGAGACCGGTGGTTGCAATTGCAACAGGAGGTGTTATTAAGGCTGCATTCGATACGATAGGTTGGGAACCCATCCTCTCCACAC

Reverse complement sequence

GTGTGGAGAGGATGGGTTCCCAACCTATCGTATCGAATGCAGCCTTAATAACACCTCCTGTTGCAATTGCAACCACCGGTCTCATCACCAAGAAGGTGGC[A/G]
CACAGTACATGTATTCTTAACCGCTCCCATGTTACACATGCCTTAATCAGCTGACAAAAGATTAAAAGCTGTCATGTTAGTTAGCCATTTAGCTAAAAAT

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 51.50% 33.60% 0.53% 14.41% NA
All Indica  2759 70.40% 5.70% 0.80% 23.05% NA
All Japonica  1512 9.30% 88.80% 0.20% 1.72% NA
Aus  269 89.20% 10.40% 0.00% 0.37% NA
Indica I  595 96.50% 3.00% 0.17% 0.34% NA
Indica II  465 82.40% 9.00% 0.43% 8.17% NA
Indica III  913 45.60% 2.80% 1.10% 50.49% NA
Indica Intermediate  786 72.50% 9.20% 1.15% 17.18% NA
Temperate Japonica  767 2.00% 97.10% 0.13% 0.78% NA
Tropical Japonica  504 20.20% 75.80% 0.40% 3.57% NA
Japonica Intermediate  241 9.50% 89.60% 0.00% 0.83% NA
VI/Aromatic  96 72.90% 25.00% 0.00% 2.08% NA
Intermediate  90 43.30% 38.90% 0.00% 17.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0612022465 T -> C LOC_Os06g20830.1 downstream_gene_variant ; 2883.0bp to feature; MODIFIER silent_mutation Average:64.193; most accessible tissue: Callus, score: 84.325 N N N N
vg0612022465 T -> C LOC_Os06g20820-LOC_Os06g20830 intergenic_region ; MODIFIER silent_mutation Average:64.193; most accessible tissue: Callus, score: 84.325 N N N N
vg0612022465 T -> DEL N N silent_mutation Average:64.193; most accessible tissue: Callus, score: 84.325 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0612022465 NA 2.07E-08 mr1242 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
vg0612022465 1.58E-07 NA mr1065_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
vg0612022465 1.10E-06 NA mr1065_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
vg0612022465 3.13E-06 NA mr1078_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
vg0612022465 2.94E-06 NA mr1087_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
vg0612022465 4.57E-07 NA mr1091_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
vg0612022465 2.91E-06 NA mr1091_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
vg0612022465 4.62E-06 NA mr1108_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
vg0612022465 5.81E-06 NA mr1110_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
vg0612022465 7.72E-06 NA mr1112_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
vg0612022465 NA 6.35E-13 mr1216_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
vg0612022465 NA 4.47E-07 mr1536_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
vg0612022465 NA 3.71E-10 mr1705_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