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Detailed information for vg0124418254:

Variant ID: vg0124418254 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 24418254
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCTTACTCATCACCTCAGCAAAAACTAGTTTTTCTGAGGAATGGACATGCCTAGGGATGTAAGCGGGACGACCTATGAACCTATTTATATGTTAAATAAA[G/A]
GGTAATCCGCGGGTTTTCACGTCATGGCTCAGCTTGCTGCGTTTATAGAAAAGCAAGTGGGTTAATATATAAACCCATTTATAAGTCAAATTAGTAGGTA

Reverse complement sequence

TACCTACTAATTTGACTTATAAATGGGTTTATATATTAACCCACTTGCTTTTCTATAAACGCAGCAAGCTGAGCCATGACGTGAAAACCCGCGGATTACC[C/T]
TTTATTTAACATATAAATAGGTTCATAGGTCGTCCCGCTTACATCCCTAGGCATGTCCATTCCTCAGAAAAACTAGTTTTTGCTGAGGTGATGAGTAAGA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	83.50%	16.50%	0.02%	0.00%	NA
All Indica	2759	96.20%	3.80%	0.00%	0.00%	NA
All Japonica	1512	73.50%	26.50%	0.07%	0.00%	NA
Aus	269	4.50%	95.50%	0.00%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	99.40%	0.60%	0.00%	0.00%	NA
Indica III	913	94.40%	5.60%	0.00%	0.00%	NA
Indica Intermediate	786	93.90%	6.10%	0.00%	0.00%	NA
Temperate Japonica	767	81.70%	18.10%	0.13%	0.00%	NA
Tropical Japonica	504	70.40%	29.60%	0.00%	0.00%	NA
Japonica Intermediate	241	53.50%	46.50%	0.00%	0.00%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	85.60%	14.40%	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
vg0124418254	G -> A	LOC_Os01g42909.1	upstream_gene_variant ; 1406.0bp to feature; MODIFIER	silent_mutation	Average:51.218; most accessible tissue: Callus, score: 85.517	N	N	N	N
vg0124418254	G -> A	LOC_Os01g42920.1	downstream_gene_variant ; 2229.0bp to feature; MODIFIER	silent_mutation	Average:51.218; most accessible tissue: Callus, score: 85.517	N	N	N	N
vg0124418254	G -> A	LOC_Os01g42909-LOC_Os01g42920	intergenic_region ; MODIFIER	silent_mutation	Average:51.218; most accessible tissue: Callus, score: 85.517	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0124418254	NA	7.06E-18	Plant_height	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
vg0124418254	NA	5.22E-06	mr1057	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
vg0124418254	NA	1.76E-09	mr1465	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
vg0124418254	NA	2.82E-14	mr1807	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
vg0124418254	NA	4.98E-07	mr1807	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
vg0124418254	4.80E-09	7.56E-26	mr1164_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
vg0124418254	NA	7.36E-08	mr1164_2	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
vg0124418254	NA	1.29E-16	mr1180_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
vg0124418254	NA	2.15E-21	mr1531_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
vg0124418254	NA	4.66E-15	mr1583_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
vg0124418254	7.06E-06	NA	mr1648_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
vg0124418254	NA	2.69E-16	mr1807_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
vg0124418254	3.17E-07	1.16E-11	mr1851_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
vg0124418254	NA	1.98E-06	mr1851_2	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