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Detailed information for vg0114526634:

Variant ID: vg0114526634 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 14526634
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


TTCTGTTTAGGGGAAATTTTAGAGTTGTGTTTTTCTGCTAGGGAATAGATGGTTCTCCAAGTTAGCTCTTATTTGTCGGACTGCAGGAATAGTTCTGCAA[A/G]
TAAGAAACACATGATCAAAACTAGAAAAGAAGCACAAAATGAAACCAGACATCTAGGAACAAGCGGTTGAACCGTTGAAGATTCACCAAATCGAGAATAT

Reverse complement sequence

ATATTCTCGATTTGGTGAATCTTCAACGGTTCAACCGCTTGTTCCTAGATGTCTGGTTTCATTTTGTGCTTCTTTTCTAGTTTTGATCATGTGTTTCTTA[T/C]
TTGCAGAACTATTCCTGCAGTCCGACAAATAAGAGCTAACTTGGAGAACCATCTATTCCCTAGCAGAAAAACACAACTCTAAAATTTCCCCTAAACAGAA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 83.20% 12.50% 0.19% 4.17% NA
All Indica  2759 71.90% 20.70% 0.33% 7.00% NA
All Japonica  1512 99.90% 0.00% 0.00% 0.07% NA
Aus  269 99.30% 0.00% 0.00% 0.74% NA
Indica I  595 94.60% 0.50% 0.17% 4.71% NA
Indica II  465 53.50% 43.40% 0.43% 2.58% NA
Indica III  913 66.30% 24.90% 0.33% 8.54% NA
Indica Intermediate  786 72.30% 17.80% 0.38% 9.54% NA
Temperate Japonica  767 99.90% 0.00% 0.00% 0.13% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 82.20% 16.70% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0114526634 A -> G LOC_Os01g25630.1 splice_region_variant&intron_variant ; LOW silent_mutation Average:43.302; most accessible tissue: Zhenshan97 flower, score: 74.953 N N N N
vg0114526634 A -> DEL N N silent_mutation Average:43.302; most accessible tissue: Zhenshan97 flower, score: 74.953 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0114526634 NA 4.85E-07 mr1183 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
vg0114526634 NA 1.24E-06 mr1503 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
vg0114526634 NA 5.24E-06 mr1830 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
vg0114526634 NA 5.78E-07 mr1428_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
vg0114526634 NA 5.22E-06 mr1654_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