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Detailed information for vg1013527440:

Variant ID: vg1013527440 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 13527440
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:

TAATACTATTGTTTGCTAACAATGATTCAAGTTGGAGATAGCTTGGTCTCGGAATATGGTTTCTTTGTTTATTTCATGTGTAGGTGACTTGATGCCTCGG[G/A]
AGAGTATTTGCGGTGATGGACCGGGAGTCGGCTTGGGGATAAGAGACGACGTCCATGGTAGTCAGAGATCATGCGGGATACTAAGGCTAGAGTTCAATAC

Reverse complement sequence

GTATTGAACTCTAGCCTTAGTATCCCGCATGATCTCTGACTACCATGGACGTCGTCTCTTATCCCCAAGCCGACTCCCGGTCCATCACCGCAAATACTCT[C/T]
CCGAGGCATCAAGTCACCTACACATGAAATAAACAAAGAAACCATATTCCGAGACCAAGCTATCTCCAACTTGAATCATTGTTAGCAAACAATAGTATTA

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	82.00%	17.50%	0.15%	0.40%	NA
All Indica	2759	69.90%	29.10%	0.25%	0.69%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	98.50%	1.50%	0.00%	0.00%	NA
Indica I	595	69.10%	29.90%	0.34%	0.67%	NA
Indica II	465	88.60%	11.00%	0.00%	0.43%	NA
Indica III	913	63.50%	35.30%	0.33%	0.88%	NA
Indica Intermediate	786	66.90%	32.20%	0.25%	0.64%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	98.60%	1.40%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	87.80%	12.20%	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
vg1013527440	G -> A	LOC_Os10g26110.1	upstream_gene_variant ; 1515.0bp to feature; MODIFIER	silent_mutation	Average:61.893; most accessible tissue: Minghui63 panicle, score: 77.956	N	N	N	N
vg1013527440	G -> A	LOC_Os10g26110-LOC_Os10g26130	intergenic_region ; MODIFIER	silent_mutation	Average:61.893; most accessible tissue: Minghui63 panicle, score: 77.956	N	N	N	N
vg1013527440	G -> DEL	N	N	silent_mutation	Average:61.893; most accessible tissue: Minghui63 panicle, score: 77.956	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1013527440	1.53E-09	NA	mr1533	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
vg1013527440	1.31E-09	2.58E-15	mr1533	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
vg1013527440	4.56E-14	NA	mr1980	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
vg1013527440	1.02E-14	4.84E-20	mr1980	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
vg1013527440	1.48E-12	NA	mr1533_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
vg1013527440	8.16E-14	5.63E-21	mr1533_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
vg1013527440	2.74E-06	NA	mr1980_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
vg1013527440	4.48E-06	3.36E-09	mr1980_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