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Detailed information for vg0113749398:

Variant ID: vg0113749398 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 13749398
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGCCATGGATAAAAACTCAACAAAAACACGAACGAATCCATGGAATAGAGAGAGGAAGCGGAGGAGAATCACTTACGGTGTAACCAGAGAGAAATCCACG[G/A]
TCAAACCGAGGGGATTTGGTGGAGAAAAGAGTTAGGGTTTGAGGGAAGGTGAGAGAGAGAGTTTTTCGAGTTGGGGATGAATCGGGATGAGATGGGAGAG

Reverse complement sequence

CTCTCCCATCTCATCCCGATTCATCCCCAACTCGAAAAACTCTCTCTCTCACCTTCCCTCAAACCCTAACTCTTTTCTCCACCAAATCCCCTCGGTTTGA[C/T]
CGTGGATTTCTCTCTGGTTACACCGTAAGTGATTCTCCTCCGCTTCCTCTCTCTATTCCATGGATTCGTTCGTGTTTTTGTTGAGTTTTTATCCATGGCA

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	41.20%	0.30%	1.21%	57.26%	NA
All Indica	2759	15.20%	0.50%	1.78%	82.53%	NA
All Japonica	1512	95.00%	0.00%	0.13%	4.83%	NA
Aus	269	7.10%	0.00%	1.86%	91.08%	NA
Indica I	595	29.90%	0.20%	0.84%	69.08%	NA
Indica II	465	11.80%	1.30%	1.29%	85.59%	NA
Indica III	913	9.70%	0.00%	2.41%	87.84%	NA
Indica Intermediate	786	12.20%	1.00%	2.04%	84.73%	NA
Temperate Japonica	767	98.40%	0.00%	0.00%	1.56%	NA
Tropical Japonica	504	88.90%	0.00%	0.20%	10.91%	NA
Japonica Intermediate	241	97.10%	0.00%	0.41%	2.49%	NA
VI/Aromatic	96	28.10%	0.00%	0.00%	71.88%	NA
Intermediate	90	52.20%	0.00%	1.11%	46.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0113749398	G -> A	LOC_Os01g24390.1	upstream_gene_variant ; 761.0bp to feature; MODIFIER	silent_mutation	Average:17.726; most accessible tissue: Callus, score: 30.807	N	N	N	N
vg0113749398	G -> A	LOC_Os01g24400.1	downstream_gene_variant ; 4105.0bp to feature; MODIFIER	silent_mutation	Average:17.726; most accessible tissue: Callus, score: 30.807	N	N	N	N
vg0113749398	G -> A	LOC_Os01g24390-LOC_Os01g24400	intergenic_region ; MODIFIER	silent_mutation	Average:17.726; most accessible tissue: Callus, score: 30.807	N	N	N	N
vg0113749398	G -> DEL	N	N	silent_mutation	Average:17.726; most accessible tissue: Callus, score: 30.807	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0113749398	4.98E-06	NA	mr1159_2	Ind_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
vg0113749398	NA	3.18E-06	mr1184_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
vg0113749398	NA	5.20E-07	mr1227_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
vg0113749398	NA	9.64E-08	mr1418_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
vg0113749398	NA	1.26E-07	mr1488_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
vg0113749398	NA	7.24E-10	mr1506_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
vg0113749398	NA	5.54E-08	mr1683_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
vg0113749398	NA	6.41E-07	mr1779_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