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Detailed information for vg0411852309:

Variant ID: vg0411852309 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 11852309
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:


TGCGACCATACTAGGTTGTTTGCTTAAGCAACTTGAATCATAAAATCCATTCACAACAGATCAATAGGCAAGTGGTTTAGTACCTCCTCTCTAGTAACCC[C/G]
TCCTATTTCCCCATCTCTCTATTGCCTGCAGCAGATGGTCCGCATGAGGGACAATTTCATCGGATCAAGACCCCGTCAGTTTCATGGGGCAACTCAGTGC

Reverse complement sequence

GCACTGAGTTGCCCCATGAAACTGACGGGGTCTTGATCCGATGAAATTGTCCCTCATGCGGACCATCTGCTGCAGGCAATAGAGAGATGGGGAAATAGGA[G/C]
GGGTTACTAGAGAGGAGGTACTAAACCACTTGCCTATTGATCTGTTGTGAATGGATTTTATGATTCAAGTTGCTTAAGCAAACAACCTAGTATGGTCGCA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 34.60% 9.30% 20.69% 35.34% NA
All Indica  2759 26.80% 15.70% 24.90% 32.58% NA
All Japonica  1512 51.40% 0.20% 2.25% 46.16% NA
Aus  269 6.30% 0.00% 81.04% 12.64% NA
Indica I  595 4.20% 30.40% 26.22% 39.16% NA
Indica II  465 41.50% 22.20% 21.08% 15.27% NA
Indica III  913 38.00% 1.80% 23.11% 37.13% NA
Indica Intermediate  786 22.30% 16.90% 28.24% 32.57% NA
Temperate Japonica  767 85.10% 0.00% 0.39% 14.47% NA
Tropical Japonica  504 5.80% 0.20% 5.36% 88.69% NA
Japonica Intermediate  241 39.40% 0.80% 1.66% 58.09% NA
VI/Aromatic  96 69.80% 0.00% 18.75% 11.46% NA
Intermediate  90 40.00% 5.60% 23.33% 31.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0411852309 C -> DEL N N silent_mutation Average:34.16; most accessible tissue: Minghui63 flag leaf, score: 64.284 N N N N
vg0411852309 C -> G LOC_Os04g21090.1 upstream_gene_variant ; 244.0bp to feature; MODIFIER silent_mutation Average:34.16; most accessible tissue: Minghui63 flag leaf, score: 64.284 N N N N
vg0411852309 C -> G LOC_Os04g21080-LOC_Os04g21090 intergenic_region ; MODIFIER silent_mutation Average:34.16; most accessible tissue: Minghui63 flag leaf, score: 64.284 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0411852309 1.43E-06 NA mr1549 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
vg0411852309 NA 2.41E-06 mr1549_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
vg0411852309 NA 7.03E-07 mr1654_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
vg0411852309 NA 4.24E-06 mr1654_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
vg0411852309 NA 5.14E-06 mr1757_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