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Detailed information for vg0421388213:

Variant ID: vg0421388213 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 21388213
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.03, others allele: 0.00, population size: 186. )

Flanking Sequence (100 bp) in Reference Genome:


TTTCACTCGTTTAAATCAGGTGTTGTTTCACCTTATATAAAAACAATGTTTCAGCAAATAGTGAAAGAATGTTTCAGTTCACTACAACATTAGATTTATA[C/T]
ATAGTGAAACATTATGATTGCACTAGGTGAAACTGTTTGATGGTATTTTGGTGATTATACATGTACACAAGACTTACTCATGATGGACAAAGCAAACAAG

Reverse complement sequence

CTTGTTTGCTTTGTCCATCATGAGTAAGTCTTGTGTACATGTATAATCACCAAAATACCATCAAACAGTTTCACCTAGTGCAATCATAATGTTTCACTAT[G/A]
TATAAATCTAATGTTGTAGTGAACTGAAACATTCTTTCACTATTTGCTGAAACATTGTTTTTATATAAGGTGAAACAACACCTGATTTAAACGAGTGAAA

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 74.00% 7.00% 2.03% 16.93% NA
All Indica  2759 61.70% 6.90% 3.30% 28.09% NA
All Japonica  1512 94.30% 5.60% 0.07% 0.07% NA
Aus  269 90.70% 4.50% 0.37% 4.46% NA
Indica I  595 76.60% 7.10% 1.51% 14.79% NA
Indica II  465 77.40% 0.90% 2.58% 19.14% NA
Indica III  913 44.60% 10.40% 3.07% 41.95% NA
Indica Intermediate  786 61.10% 6.20% 5.34% 27.35% NA
Temperate Japonica  767 93.40% 6.50% 0.13% 0.00% NA
Tropical Japonica  504 93.10% 6.70% 0.00% 0.20% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 54.20% 40.60% 1.04% 4.17% NA
Intermediate  90 81.10% 7.80% 2.22% 8.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0421388213 C -> DEL N N silent_mutation Average:51.268; most accessible tissue: Callus, score: 77.392 N N N N
vg0421388213 C -> T LOC_Os04g35200.1 upstream_gene_variant ; 621.0bp to feature; MODIFIER silent_mutation Average:51.268; most accessible tissue: Callus, score: 77.392 N N N N
vg0421388213 C -> T LOC_Os04g35190.1 downstream_gene_variant ; 2861.0bp to feature; MODIFIER silent_mutation Average:51.268; most accessible tissue: Callus, score: 77.392 N N N N
vg0421388213 C -> T LOC_Os04g35200-LOC_Os04g35210 intergenic_region ; MODIFIER silent_mutation Average:51.268; most accessible tissue: Callus, score: 77.392 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0421388213 4.74E-06 4.74E-06 mr1108_2 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