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Detailed information for vg1221706812:

Variant ID: vg1221706812 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 21706812
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CACACGTAGATGAGTCTTTAACTTGTTTATGAGAGATAATAACAGAGCTAGTGTGACTAAAATCACCTGCATGAAATTAATTAACAGTATTCCCTATACA[G/A]
TAGTATATGTTTAGGTTGCAAATCGACCCTTAAGTTGTATAGACGGTAATTCACTCATAAATCCACTTAAAATCACATGTACTATATAGCCTATAGTAAA

Reverse complement sequence

TTTACTATAGGCTATATAGTACATGTGATTTTAAGTGGATTTATGAGTGAATTACCGTCTATACAACTTAAGGGTCGATTTGCAACCTAAACATATACTA[C/T]
TGTATAGGGAATACTGTTAATTAATTTCATGCAGGTGATTTTAGTCACACTAGCTCTGTTATTATCTCTCATAAACAAGTTAAAGACTCATCTACGTGTG

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 98.10% 1.70% 0.21% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 93.90% 5.40% 0.66% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 91.40% 7.60% 1.04% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 90.00% 9.10% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg1221706812 G -> A LOC_Os12g35700.1 upstream_gene_variant ; 2960.0bp to feature; MODIFIER silent_mutation Average:28.056; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N
vg1221706812 G -> A LOC_Os12g35710.1 downstream_gene_variant ; 4428.0bp to feature; MODIFIER silent_mutation Average:28.056; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N
vg1221706812 G -> A LOC_Os12g35700-LOC_Os12g35710 intergenic_region ; MODIFIER silent_mutation Average:28.056; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1221706812 NA 9.78E-06 mr1210 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
vg1221706812 NA 3.87E-06 mr1305 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
vg1221706812 NA 4.74E-07 mr1515 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
vg1221706812 NA 8.86E-06 mr1836 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
vg1221706812 4.83E-07 4.83E-07 mr1967 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