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Detailed information for vg0318063509:

Variant ID: vg0318063509 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 18063509
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACAAGGAGATCTTGTAATTTCTCATAAGATCAGCTAAGCACAGGAGTAGGGTATTACGCTTCTTATTGGCCCGAACCTATATAAACTCCTTTTGTCTCAT[C/T]
GTCTTTGAGGGGGCTGACCCCTTAATGTCACACAACTTTGCTCACCAAGCCCTCAAATCTCACCCGCTGCCCCCGGCCGAACCAAAAAAGAGGGCCTCAT

Reverse complement sequence

ATGAGGCCCTCTTTTTTGGTTCGGCCGGGGGCAGCGGGTGAGATTTGAGGGCTTGGTGAGCAAAGTTGTGTGACATTAAGGGGTCAGCCCCCTCAAAGAC[G/A]
ATGAGACAAAAGGAGTTTATATAGGTTCGGGCCAATAAGAAGCGTAATACCCTACTCCTGTGCTTAGCTGATCTTATGAGAAATTACAAGATCTCCTTGT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 68.60% 30.90% 0.08% 0.44% NA
All Indica  2759 97.60% 1.90% 0.00% 0.47% NA
All Japonica  1512 14.70% 85.10% 0.07% 0.20% NA
Aus  269 92.90% 7.10% 0.00% 0.00% NA
Indica I  595 97.80% 1.20% 0.00% 1.01% NA
Indica II  465 97.00% 2.60% 0.00% 0.43% NA
Indica III  913 98.90% 1.00% 0.00% 0.11% NA
Indica Intermediate  786 96.40% 3.10% 0.00% 0.51% NA
Temperate Japonica  767 0.50% 99.30% 0.00% 0.13% NA
Tropical Japonica  504 39.50% 60.10% 0.00% 0.40% NA
Japonica Intermediate  241 7.90% 91.70% 0.41% 0.00% NA
VI/Aromatic  96 25.00% 71.90% 3.12% 0.00% NA
Intermediate  90 55.60% 38.90% 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
vg0318063509 C -> T LOC_Os03g31640.1 upstream_gene_variant ; 3619.0bp to feature; MODIFIER silent_mutation Average:66.641; most accessible tissue: Minghui63 panicle, score: 77.956 N N N N
vg0318063509 C -> T LOC_Os03g31634.1 downstream_gene_variant ; 2280.0bp to feature; MODIFIER silent_mutation Average:66.641; most accessible tissue: Minghui63 panicle, score: 77.956 N N N N
vg0318063509 C -> T LOC_Os03g31634-LOC_Os03g31640 intergenic_region ; MODIFIER silent_mutation Average:66.641; most accessible tissue: Minghui63 panicle, score: 77.956 N N N N
vg0318063509 C -> DEL N N silent_mutation Average:66.641; most accessible tissue: Minghui63 panicle, score: 77.956 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0318063509 NA 1.89E-09 mr1198 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
vg0318063509 NA 6.38E-06 mr1215 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
vg0318063509 NA 6.46E-22 mr1217 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
vg0318063509 NA 8.48E-08 mr1217 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
vg0318063509 NA 1.31E-08 mr1275 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
vg0318063509 NA 1.15E-17 mr1304 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
vg0318063509 NA 2.02E-14 mr1376 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
vg0318063509 NA 2.02E-14 mr1431 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
vg0318063509 NA 4.17E-06 mr1583 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
vg0318063509 NA 4.18E-09 mr1607 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
vg0318063509 NA 3.25E-10 mr1718 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
vg0318063509 8.70E-08 7.36E-20 mr1750 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
vg0318063509 NA 7.54E-07 mr1830 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
vg0318063509 NA 1.43E-19 mr1845 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
vg0318063509 NA 6.94E-07 mr1845 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
vg0318063509 NA 1.41E-08 mr1852 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
vg0318063509 2.06E-07 2.06E-07 mr1987 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
vg0318063509 NA 5.83E-09 mr1136_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
vg0318063509 NA 5.80E-15 mr1718_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
vg0318063509 4.05E-08 NA mr1750_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
vg0318063509 7.73E-21 1.27E-37 mr1750_2 Ind_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
vg0318063509 NA 1.83E-08 mr1800_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
vg0318063509 NA 1.08E-07 mr1987_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