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Detailed information for vg0414197719:

Variant ID: vg0414197719 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 14197719
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.05, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:


TTACATAAATGTGGAACTAGTTCAGTATTTATAAATGATGTGCAACTGGTTCATTATTTCTAACAAATGTGCATCTTGTTAAATACTCTTAATAAATGTG[T/C]
AACTGGTTAAATAATTTTAATTGCCTTGATTATTTGTGGAACAGGCGGAATTTGTTGAGCATGTTCACGTGGAGTCCGACACCCTACTGCAAAGACTAGA

Reverse complement sequence

TCTAGTCTTTGCAGTAGGGTGTCGGACTCCACGTGAACATGCTCAACAAATTCCGCCTGTTCCACAAATAATCAAGGCAATTAAAATTATTTAACCAGTT[A/G]
CACATTTATTAAGAGTATTTAACAAGATGCACATTTGTTAGAAATAATGAACCAGTTGCACATCATTTATAAATACTGAACTAGTTCCACATTTATGTAA

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 13.80% 11.80% 4.89% 69.47% NA
All Indica  2759 7.40% 4.30% 3.23% 85.07% NA
All Japonica  1512 28.20% 21.20% 5.62% 44.91% NA
Aus  269 0.40% 37.90% 7.43% 54.28% NA
Indica I  595 23.50% 9.40% 3.70% 63.36% NA
Indica II  465 0.90% 1.70% 3.01% 94.41% NA
Indica III  913 1.60% 3.20% 2.63% 92.55% NA
Indica Intermediate  786 5.70% 3.30% 3.69% 87.28% NA
Temperate Japonica  767 46.00% 40.20% 7.17% 6.65% NA
Tropical Japonica  504 2.40% 0.20% 1.59% 95.83% NA
Japonica Intermediate  241 25.70% 5.00% 9.13% 60.17% NA
VI/Aromatic  96 9.40% 6.20% 31.25% 53.12% NA
Intermediate  90 13.30% 12.20% 7.78% 66.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0414197719 T -> C LOC_Os04g24730.1 intron_variant ; MODIFIER silent_mutation Average:7.253; most accessible tissue: Callus, score: 18.519 N N N N
vg0414197719 T -> DEL N N silent_mutation Average:7.253; most accessible tissue: Callus, score: 18.519 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0414197719 NA 8.63E-09 mr1054 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
vg0414197719 NA 2.90E-07 mr1062 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
vg0414197719 NA 4.44E-08 mr1287 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
vg0414197719 NA 2.79E-07 mr1328 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
vg0414197719 NA 3.56E-06 mr1345 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
vg0414197719 NA 6.35E-06 mr1353 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
vg0414197719 NA 5.21E-08 mr1372 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
vg0414197719 NA 9.37E-07 mr1400 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
vg0414197719 NA 1.94E-09 mr1403 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
vg0414197719 NA 7.29E-06 mr1427 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
vg0414197719 NA 2.75E-07 mr1432 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
vg0414197719 NA 7.30E-06 mr1433 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
vg0414197719 NA 2.41E-07 mr1512 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
vg0414197719 NA 9.47E-06 mr1525 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
vg0414197719 NA 2.61E-07 mr1545 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
vg0414197719 NA 2.29E-08 mr1585 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
vg0414197719 NA 7.30E-07 mr1596 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
vg0414197719 NA 1.76E-06 mr1634 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
vg0414197719 NA 3.83E-06 mr1774 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
vg0414197719 NA 1.74E-11 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
vg0414197719 NA 2.54E-07 mr1582_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