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Detailed information for vg1221719215:

Variant ID: vg1221719215 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 21719215
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:


TTCGTCGGATGAAGAAATAACAAAAATAAAAGTTTTAGATCTTGATGAGTTATTCAACTTTGTTGTTGATGACTTTTTCAATTGAAATCATTTAGTATTT[A/G]
AAAATGTTGTTTGAAGTTGTCATATTTTTAAATTCAAATTCAAGTTGTTCAATAAAATGTTATATTGAAAAATGACCAAACTAAAAGTTGTAAATCTTGA

Reverse complement sequence

TCAAGATTTACAACTTTTAGTTTGGTCATTTTTCAATATAACATTTTATTGAACAACTTGAATTTGAATTTAAAAATATGACAACTTCAAACAACATTTT[T/C]
AAATACTAAATGATTTCAATTGAAAAAGTCATCAACAACAAAGTTGAATAACTCATCAAGATCTAAAACTTTTATTTTTGTTATTTCTTCATCCGACGAA

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 68.90% 24.30% 6.41% 0.44% NA
All Indica  2759 85.20% 3.60% 10.47% 0.72% NA
All Japonica  1512 38.80% 60.80% 0.40% 0.00% NA
Aus  269 88.10% 10.80% 1.12% 0.00% NA
Indica I  595 78.80% 3.20% 15.46% 2.52% NA
Indica II  465 85.40% 5.40% 9.25% 0.00% NA
Indica III  913 89.40% 2.10% 8.43% 0.11% NA
Indica Intermediate  786 85.00% 4.70% 9.80% 0.51% NA
Temperate Japonica  767 28.80% 70.70% 0.52% 0.00% NA
Tropical Japonica  504 39.70% 60.10% 0.20% 0.00% NA
Japonica Intermediate  241 68.90% 30.70% 0.41% 0.00% NA
VI/Aromatic  96 41.70% 57.30% 0.00% 1.04% NA
Intermediate  90 45.60% 48.90% 5.56% 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
vg1221719215 A -> DEL N N silent_mutation Average:17.897; most accessible tissue: Minghui63 panicle, score: 25.313 N N N N
vg1221719215 A -> G LOC_Os12g35710-LOC_Os12g35720 intergenic_region ; MODIFIER silent_mutation Average:17.897; most accessible tissue: Minghui63 panicle, score: 25.313 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1221719215 NA 1.14E-08 mr1198_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
vg1221719215 NA 1.63E-06 mr1272_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
vg1221719215 NA 1.28E-07 mr1275_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
vg1221719215 NA 1.77E-06 mr1289_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
vg1221719215 NA 3.46E-10 mr1349_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
vg1221719215 NA 5.01E-06 mr1405_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
vg1221719215 NA 3.73E-06 mr1407_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
vg1221719215 3.83E-06 3.40E-14 mr1575_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
vg1221719215 NA 4.65E-06 mr1869_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
vg1221719215 NA 6.58E-08 mr1909_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
vg1221719215 NA 5.50E-08 mr1921_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
vg1221719215 NA 2.83E-09 mr1940_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