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Detailed information for vg0419568634:

Variant ID: vg0419568634 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 19568634
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.87, T: 0.13, others allele: 0.00, population size: 119. )

Flanking Sequence (100 bp) in Reference Genome:


CATTTTTTTTCAAAAGTAAAAAATTTAAAGCCTGGATGAAACACTTAATATTTAGTTCTTTTTATTTGCGGGTGCTCGATAAAACACTTGATGGGTATTC[T/C]
TGGAATTAAAAATCACATGCGTTTAATTTTCAAATAATCACAAAACCCACAAATATTGCCTTAATTAAAATCGATATTGAGGTTTGCTTTTAGGAAAAAA

Reverse complement sequence

TTTTTTCCTAAAAGCAAACCTCAATATCGATTTTAATTAAGGCAATATTTGTGGGTTTTGTGATTATTTGAAAATTAAACGCATGTGATTTTTAATTCCA[A/G]
GAATACCCATCAAGTGTTTTATCGAGCACCCGCAAATAAAAAGAACTAAATATTAAGTGTTTCATCCAGGCTTTAAATTTTTTACTTTTGAAAAAAAATG

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 59.90% 39.40% 0.36% 0.38% NA
All Indica  2759 92.80% 6.60% 0.22% 0.40% NA
All Japonica  1512 4.00% 95.20% 0.60% 0.20% NA
Aus  269 69.90% 30.10% 0.00% 0.00% NA
Indica I  595 89.40% 8.90% 0.67% 1.01% NA
Indica II  465 90.80% 8.80% 0.00% 0.43% NA
Indica III  913 98.10% 1.90% 0.00% 0.00% NA
Indica Intermediate  786 90.20% 9.20% 0.25% 0.38% NA
Temperate Japonica  767 6.60% 92.20% 1.17% 0.00% NA
Tropical Japonica  504 0.60% 99.20% 0.00% 0.20% NA
Japonica Intermediate  241 2.50% 96.70% 0.00% 0.83% NA
VI/Aromatic  96 2.10% 97.90% 0.00% 0.00% NA
Intermediate  90 22.20% 71.10% 2.22% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0419568634 T -> C LOC_Os04g32510.1 downstream_gene_variant ; 2314.0bp to feature; MODIFIER silent_mutation Average:43.299; most accessible tissue: Minghui63 root, score: 69.846 N N N N
vg0419568634 T -> C LOC_Os04g32510-LOC_Os04g32540 intergenic_region ; MODIFIER silent_mutation Average:43.299; most accessible tissue: Minghui63 root, score: 69.846 N N N N
vg0419568634 T -> DEL N N silent_mutation Average:43.299; most accessible tissue: Minghui63 root, score: 69.846 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0419568634 NA 1.81E-06 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
vg0419568634 NA 7.16E-10 mr1151 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
vg0419568634 NA 1.15E-08 mr1174 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
vg0419568634 NA 4.73E-10 mr1307 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
vg0419568634 NA 1.71E-06 mr1315 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
vg0419568634 4.03E-06 NA mr1347 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
vg0419568634 1.36E-06 1.36E-06 mr1461 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
vg0419568634 NA 1.35E-12 mr1521 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
vg0419568634 NA 6.77E-08 mr1646 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
vg0419568634 7.91E-06 4.60E-06 mr1741 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
vg0419568634 NA 9.32E-09 mr1776 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
vg0419568634 NA 3.15E-07 mr1824 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
vg0419568634 NA 2.11E-07 mr1851 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
vg0419568634 NA 3.90E-07 mr1321_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
vg0419568634 NA 2.94E-10 mr1349_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
vg0419568634 NA 2.38E-08 mr1489_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
vg0419568634 NA 7.45E-07 mr1568_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