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Detailed information for vg0225012379:

Variant ID: vg0225012379 (JBrowse)Variation Type: INDEL
Chromosome: chr02Position: 25012379
Reference Allele: TAlternative Allele: C,TGGAAACAGC
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACTTTTTAGTTTCCGAAATTTTTTTTGTGTTACATCGGATGTCGGAAGGGGTTTTTGCACATAAATAAAAAAACTAATTTCATAACTCGCCTGTAAACCG[T/C,TGGAAACAGC]
GAGACGAATCTTTTGAGCCTAATTAATCCGTCCTTAGCACGTGTGTGTTTCTATAGCACTTATAGCTAATCATGGACAAATTAGGCTCAAAAGATTCATC

Reverse complement sequence

GATGAATCTTTTGAGCCTAATTTGTCCATGATTAGCTATAAGTGCTATAGAAACACACACGTGCTAAGGACGGATTAATTAGGCTCAAAAGATTCGTCTC[A/G,GCTGTTTCCA]
CGGTTTACAGGCGAGTTATGAAATTAGTTTTTTTATTTATGTGCAAAAACCCCTTCCGACATCCGATGTAACACAAAAAAAATTTCGGAAACTAAAAAGT

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 49.00% 37.00% 0.06% 0.00% TGGAAACAGC: 13.99%
All Indica  2759 74.10% 9.60% 0.11% 0.00% TGGAAACAGC: 16.24%
All Japonica  1512 8.70% 90.90% 0.00% 0.00% TGGAAACAGC: 0.46%
Aus  269 16.70% 15.20% 0.00% 0.00% TGGAAACAGC: 68.03%
Indica I  595 91.40% 7.90% 0.17% 0.00% TGGAAACAGC: 0.50%
Indica II  465 58.90% 3.90% 0.00% 0.00% TGGAAACAGC: 37.20%
Indica III  913 78.00% 9.90% 0.00% 0.00% TGGAAACAGC: 12.16%
Indica Intermediate  786 65.40% 13.90% 0.25% 0.00% TGGAAACAGC: 20.48%
Temperate Japonica  767 7.40% 92.40% 0.00% 0.00% TGGAAACAGC: 0.13%
Tropical Japonica  504 12.30% 87.50% 0.00% 0.00% TGGAAACAGC: 0.20%
Japonica Intermediate  241 5.00% 92.90% 0.00% 0.00% TGGAAACAGC: 2.07%
VI/Aromatic  96 62.50% 26.00% 0.00% 0.00% TGGAAACAGC: 11.46%
Intermediate  90 37.80% 48.90% 0.00% 0.00% TGGAAACAGC: 13.33%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0225012379 T -> TGGAAACAGC LOC_Os02g41680.1 upstream_gene_variant ; 3259.0bp to feature; MODIFIER silent_mutation Average:31.95; most accessible tissue: Minghui63 root, score: 56.226 N N N N
vg0225012379 T -> TGGAAACAGC LOC_Os02g41680-LOC_Os02g41690 intergenic_region ; MODIFIER silent_mutation Average:31.95; most accessible tissue: Minghui63 root, score: 56.226 N N N N
vg0225012379 T -> C LOC_Os02g41680.1 upstream_gene_variant ; 3258.0bp to feature; MODIFIER silent_mutation Average:31.95; most accessible tissue: Minghui63 root, score: 56.226 N N N N
vg0225012379 T -> C LOC_Os02g41680-LOC_Os02g41690 intergenic_region ; MODIFIER silent_mutation Average:31.95; most accessible tissue: Minghui63 root, score: 56.226 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0225012379 NA 8.78E-07 mr1077 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
vg0225012379 NA 7.47E-06 mr1174 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
vg0225012379 NA 1.67E-11 mr1195 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
vg0225012379 NA 1.04E-19 mr1253 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
vg0225012379 NA 5.89E-07 mr1321 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
vg0225012379 NA 2.49E-10 mr1342 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
vg0225012379 NA 2.20E-09 mr1379 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
vg0225012379 NA 2.91E-06 mr1555 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
vg0225012379 4.33E-06 7.96E-16 mr1655 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
vg0225012379 NA 9.89E-09 mr1717 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
vg0225012379 NA 4.63E-06 mr1876 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
vg0225012379 NA 1.24E-10 mr1927 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
vg0225012379 NA 8.99E-06 mr1098_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
vg0225012379 7.61E-06 8.22E-08 mr1150_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