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Detailed information for vg1206249313:

Variant ID: vg1206249313 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 6249313
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.61, A: 0.39, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:


ATTTCATATTTCCATAAACTGTCAGTGAATCCTTCCTTTTGGTTGACGTTTTTGTCATCCGACAACATTTCAGTTAGGGAAAAGTTGTACGTTTAGCAGT[G/A]
AGAGGTAGGGTGGGTGCTCCTTGGCTAAAAACCCATGAAATTAATGCTTCCATTGACACCGAGATAGATAGTTTGATAGGTCCTACACCGAGATATATAG

Reverse complement sequence

CTATATATCTCGGTGTAGGACCTATCAAACTATCTATCTCGGTGTCAATGGAAGCATTAATTTCATGGGTTTTTAGCCAAGGAGCACCCACCCTACCTCT[C/T]
ACTGCTAAACGTACAACTTTTCCCTAACTGAAATGTTGTCGGATGACAAAAACGTCAACCAAAAGGAAGGATTCACTGACAGTTTATGGAAATATGAAAT

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 43.10% 32.00% 1.35% 23.61% NA
All Indica  2759 45.10% 51.70% 0.69% 2.46% NA
All Japonica  1512 30.60% 4.00% 1.92% 63.49% NA
Aus  269 72.90% 1.10% 2.23% 23.79% NA
Indica I  595 94.60% 4.00% 0.34% 1.01% NA
Indica II  465 23.00% 74.00% 1.08% 1.94% NA
Indica III  913 20.40% 76.60% 0.66% 2.41% NA
Indica Intermediate  786 49.50% 45.80% 0.76% 3.94% NA
Temperate Japonica  767 40.70% 5.30% 1.96% 52.02% NA
Tropical Japonica  504 10.10% 3.60% 2.58% 83.73% NA
Japonica Intermediate  241 41.50% 0.40% 0.41% 57.68% NA
VI/Aromatic  96 87.50% 1.00% 9.38% 2.08% NA
Intermediate  90 53.30% 21.10% 1.11% 24.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1206249313 G -> DEL N N silent_mutation Average:35.073; most accessible tissue: Minghui63 flag leaf, score: 57.188 N N N N
vg1206249313 G -> A LOC_Os12g11530-LOC_Os12g11550 intergenic_region ; MODIFIER silent_mutation Average:35.073; most accessible tissue: Minghui63 flag leaf, score: 57.188 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1206249313 NA 1.82E-10 Grain_width Ind_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1206249313 2.39E-06 NA mr1134 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
vg1206249313 NA 1.59E-06 mr1180 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
vg1206249313 1.10E-06 NA mr1504 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
vg1206249313 NA 5.62E-12 mr1565 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
vg1206249313 1.07E-06 1.01E-06 mr1940 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
vg1206249313 NA 8.00E-06 mr1329_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
vg1206249313 NA 1.48E-13 mr1565_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
vg1206249313 NA 2.44E-11 mr1565_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
vg1206249313 NA 1.46E-10 mr1861_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