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Detailed information for vg0402019968:

Variant ID: vg0402019968 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 2019968
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 327. )

Flanking Sequence (100 bp) in Reference Genome:


CTACCCTGACCTCGATCATGAACTTTGAAGCGATTAGTTTGACCAGAAAACTTATCGTCCGACTAATCACGACTAGTCATGAGAGTCGATCAAATTAGTC[G/A]
TGGATGACTAGTCTGTTAGGGCTAAAAATATGTGTTGGACTTTACACTTCAGTGGCAGGCCTTTTGCCCAGCCCAAGAAGGCCTGTACCCCTCATCTAAC

Reverse complement sequence

GTTAGATGAGGGGTACAGGCCTTCTTGGGCTGGGCAAAAGGCCTGCCACTGAAGTGTAAAGTCCAACACATATTTTTAGCCCTAACAGACTAGTCATCCA[C/T]
GACTAATTTGATCGACTCTCATGACTAGTCGTGATTAGTCGGACGATAAGTTTTCTGGTCAAACTAATCGCTTCAAAGTTCATGATCGAGGTCAGGGTAG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 86.10% 13.90% 0.00% 0.00% NA
All Indica  2759 84.90% 15.10% 0.00% 0.00% NA
All Japonica  1512 84.90% 15.10% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 95.60% 4.40% 0.00% 0.00% NA
Indica II  465 72.00% 28.00% 0.00% 0.00% NA
Indica III  913 83.40% 16.60% 0.00% 0.00% NA
Indica Intermediate  786 86.10% 13.90% 0.00% 0.00% NA
Temperate Japonica  767 98.20% 1.80% 0.00% 0.00% NA
Tropical Japonica  504 67.50% 32.50% 0.00% 0.00% NA
Japonica Intermediate  241 79.30% 20.70% 0.00% 0.00% NA
VI/Aromatic  96 94.80% 5.20% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0402019968 G -> A LOC_Os04g04310.1 upstream_gene_variant ; 1163.0bp to feature; MODIFIER silent_mutation Average:68.393; most accessible tissue: Zhenshan97 panicle, score: 82.888 N N N N
vg0402019968 G -> A LOC_Os04g04300.1 downstream_gene_variant ; 2236.0bp to feature; MODIFIER silent_mutation Average:68.393; most accessible tissue: Zhenshan97 panicle, score: 82.888 N N N N
vg0402019968 G -> A LOC_Os04g04320.1 intron_variant ; MODIFIER silent_mutation Average:68.393; most accessible tissue: Zhenshan97 panicle, score: 82.888 N N N N
vg0402019968 G -> A LOC_Os04g04320.2 intron_variant ; MODIFIER silent_mutation Average:68.393; most accessible tissue: Zhenshan97 panicle, score: 82.888 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0402019968 1.79E-07 NA mr1798_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
vg0402019968 3.91E-11 NA mr1798_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