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Detailed information for vg0606938203:

Variant ID: vg0606938203 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 6938203
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTCTAAACTTGTATGGCAAGAAAATACCCGGGATCCTAGTCGGCTACGATTGTATTTTATCTGTAATCCCATATTCTGTTAGGATATGGACTGTACCTT[G/A]
TATTACGGATCCCTTCTCCTATATAAGGAGGGTCCGTGTGCCTCTTGGGGCACGTTTTTCTTTTTTTTTCCCAATCATACAATCAATAACACACTCGGCG

Reverse complement sequence

CGCCGAGTGTGTTATTGATTGTATGATTGGGAAAAAAAAAGAAAAACGTGCCCCAAGAGGCACACGGACCCTCCTTATATAGGAGAAGGGATCCGTAATA[C/T]
AAGGTACAGTCCATATCCTAACAGAATATGGGATTACAGATAAAATACAATCGTAGCCGACTAGGATCCCGGGTATTTTCTTGCCATACAAGTTTAGAAT

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 83.00% 17.00% 0.00% 0.00% NA
All Indica  2759 80.30% 19.70% 0.00% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 8.20% 91.80% 0.00% 0.00% NA
Indica I  595 95.80% 4.20% 0.00% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 56.30% 43.70% 0.00% 0.00% NA
Indica Intermediate  786 85.40% 14.60% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 94.80% 5.20% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg0606938203 G -> A LOC_Os06g12700.1 upstream_gene_variant ; 835.0bp to feature; MODIFIER silent_mutation Average:31.39; most accessible tissue: Zhenshan97 panicle, score: 69.946 N N N N
vg0606938203 G -> A LOC_Os06g12710.1 upstream_gene_variant ; 292.0bp to feature; MODIFIER silent_mutation Average:31.39; most accessible tissue: Zhenshan97 panicle, score: 69.946 N N N N
vg0606938203 G -> A LOC_Os06g12700-LOC_Os06g12710 intergenic_region ; MODIFIER silent_mutation Average:31.39; most accessible tissue: Zhenshan97 panicle, score: 69.946 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0606938203 NA 5.53E-08 mr1970 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
vg0606938203 NA 1.41E-10 mr1973 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
vg0606938203 4.61E-06 NA mr1933_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
vg0606938203 NA 1.28E-11 mr1970_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
vg0606938203 9.03E-06 5.87E-14 mr1973_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