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Detailed information for vg0421497707:

Variant ID: vg0421497707 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 21497707
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

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

Flanking Sequence (100 bp) in Reference Genome:


ATGAAGCACACGGTCGTTAGTTAATGACAAATATCATTGTTTTTTTTATTCCTGGTTCTGATTCATTATTGGATCATGTTTCACCATTCAGAGTGTGTCC[C/T]
GTGGTGTTTTCTTTTCGTGCAGAACCATGTGGTTCATTTGTATTTTTGAGTCTTTCCTTAAGTGCATCTCTGTACGTTTACATGTTTTTTTTTTTGTCCC

Reverse complement sequence

GGGACAAAAAAAAAAACATGTAAACGTACAGAGATGCACTTAAGGAAAGACTCAAAAATACAAATGAACCACATGGTTCTGCACGAAAAGAAAACACCAC[G/A]
GGACACACTCTGAATGGTGAAACATGATCCAATAATGAATCAGAACCAGGAATAAAAAAAACAATGATATTTGTCATTAACTAACGACCGTGTGCTTCAT

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 49.20% 0.80% 14.71% 35.27% NA
All Indica  2759 49.70% 1.20% 15.30% 33.82% NA
All Japonica  1512 52.10% 0.00% 3.51% 44.44% NA
Aus  269 29.70% 1.10% 58.74% 10.41% NA
Indica I  595 78.70% 0.30% 6.05% 14.96% NA
Indica II  465 71.60% 1.70% 5.38% 21.29% NA
Indica III  913 21.90% 1.50% 23.44% 53.12% NA
Indica Intermediate  786 46.90% 1.30% 18.70% 33.08% NA
Temperate Japonica  767 75.10% 0.00% 1.96% 22.95% NA
Tropical Japonica  504 20.20% 0.00% 5.56% 74.21% NA
Japonica Intermediate  241 45.20% 0.00% 4.15% 50.62% NA
VI/Aromatic  96 40.60% 1.00% 43.75% 14.58% NA
Intermediate  90 53.30% 2.20% 22.22% 22.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0421497707 C -> DEL N N silent_mutation Average:36.308; most accessible tissue: Zhenshan97 flower, score: 76.539 N N N N
vg0421497707 C -> T LOC_Os04g35340.1 upstream_gene_variant ; 3465.0bp to feature; MODIFIER silent_mutation Average:36.308; most accessible tissue: Zhenshan97 flower, score: 76.539 N N N N
vg0421497707 C -> T LOC_Os04g35340-LOC_Os04g35370 intergenic_region ; MODIFIER silent_mutation Average:36.308; most accessible tissue: Zhenshan97 flower, score: 76.539 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0421497707 NA 3.22E-06 mr1277 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
vg0421497707 8.89E-06 NA mr1200_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
vg0421497707 2.16E-06 2.16E-06 mr1303_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
vg0421497707 6.60E-06 NA mr1304_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
vg0421497707 7.05E-06 7.05E-06 mr1424_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
vg0421497707 2.37E-06 NA mr1551_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
vg0421497707 5.25E-06 NA mr1612_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
vg0421497707 5.76E-06 NA mr1757_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
vg0421497707 NA 3.48E-07 mr1762_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
vg0421497707 NA 6.21E-06 mr1790_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
vg0421497707 9.11E-07 5.10E-08 mr1819_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