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Detailed information for vg0410309978:

Variant ID: vg0410309978 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 10309978
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:


CGAAGGGGTACGAAGGGTGCTTGAATAGATGTCAAAATGTTCGGTCCTTAACGACTCAGACCGGGCTACTTGCATCAGAGGAAAACCAACCTCCCTTCAT[T/C]
GCCCTATCACCCGTCCAAGTCCAACATATTTCATCAACCATTATTTAGCGTAAGTGCTCAAGTTTTATGCCCAATAATGCAAGTTGTCTATATACCACAA

Reverse complement sequence

TTGTGGTATATAGACAACTTGCATTATTGGGCATAAAACTTGAGCACTTACGCTAAATAATGGTTGATGAAATATGTTGGACTTGGACGGGTGATAGGGC[A/G]
ATGAAGGGAGGTTGGTTTTCCTCTGATGCAAGTAGCCCGGTCTGAGTCGTTAAGGACCGAACATTTTGACATCTATTCAAGCACCCTTCGTACCCCTTCG

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 76.50% 20.40% 0.51% 2.60% NA
All Indica  2759 99.20% 0.80% 0.00% 0.04% NA
All Japonica  1512 33.90% 61.00% 1.46% 3.64% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.30% 0.70% 0.00% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 98.60% 1.30% 0.00% 0.13% NA
Temperate Japonica  767 3.70% 96.00% 0.13% 0.26% NA
Tropical Japonica  504 83.30% 4.40% 3.77% 8.53% NA
Japonica Intermediate  241 27.00% 68.00% 0.83% 4.15% NA
VI/Aromatic  96 33.30% 0.00% 2.08% 64.58% NA
Intermediate  90 74.40% 20.00% 0.00% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0410309978 T -> C LOC_Os04g18640.1 upstream_gene_variant ; 2450.0bp to feature; MODIFIER silent_mutation Average:43.75; most accessible tissue: Minghui63 flag leaf, score: 63.086 N N N N
vg0410309978 T -> C LOC_Os04g18640-LOC_Os04g18650 intergenic_region ; MODIFIER silent_mutation Average:43.75; most accessible tissue: Minghui63 flag leaf, score: 63.086 N N N N
vg0410309978 T -> DEL N N silent_mutation Average:43.75; most accessible tissue: Minghui63 flag leaf, score: 63.086 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0410309978 NA 2.58E-07 mr1194 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
vg0410309978 NA 2.18E-34 mr1310 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
vg0410309978 NA 3.74E-08 mr1449 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
vg0410309978 NA 2.12E-11 mr1650 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
vg0410309978 NA 5.08E-07 mr1715 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
vg0410309978 NA 8.71E-09 mr1746 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
vg0410309978 NA 2.46E-31 mr1789 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
vg0410309978 NA 6.15E-13 mr1844 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
vg0410309978 NA 2.06E-40 mr1926 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
vg0410309978 NA 8.30E-11 mr1959 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
vg0410309978 NA 6.41E-06 mr1211_2 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
vg0410309978 NA 5.82E-10 mr1282_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
vg0410309978 3.71E-08 NA mr1758_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