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Detailed information for vg1001913135:

Variant ID: vg1001913135 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 1913135
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGTGCACACAGAAACACTCACAAAAAGCGAATAGTGCATGTTTTGTATGAGATGCGCAAACATGTTGGTAATCGAGAGGAATTTGACATAAAGGCAAATA[T/A]
AAATCTTGCTCATCTTGATATGTTGGACAAAAGCTCCCTATGCTTATTTCTGCACATAACAGTTTTTCAAGTAAACTTACTGCGGAAAAAATGCCTCCGT

Reverse complement sequence

ACGGAGGCATTTTTTCCGCAGTAAGTTTACTTGAAAAACTGTTATGTGCAGAAATAAGCATAGGGAGCTTTTGTCCAACATATCAAGATGAGCAAGATTT[A/T]
TATTTGCCTTTATGTCAAATTCCTCTCGATTACCAACATGTTTGCGCATCTCATACAAAACATGCACTATTCGCTTTTTGTGAGTGTTTCTGTGTGCACA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	83.30%	0.20%	0.68%	15.83%	NA
All Indica	2759	75.80%	0.40%	0.22%	23.63%	NA
All Japonica	1512	99.50%	0.00%	0.00%	0.46%	NA
Aus	269	60.60%	0.40%	9.67%	29.37%	NA
Indica I	595	57.60%	0.00%	0.17%	42.18%	NA
Indica II	465	82.80%	0.40%	0.00%	16.77%	NA
Indica III	913	79.60%	0.70%	0.33%	19.39%	NA
Indica Intermediate	786	80.90%	0.30%	0.25%	18.58%	NA
Temperate Japonica	767	99.20%	0.00%	0.00%	0.78%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	95.80%	0.00%	0.00%	4.17%	NA
Intermediate	90	93.30%	0.00%	0.00%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1001913135	T -> A	LOC_Os10g04120.1	upstream_gene_variant ; 3819.0bp to feature; MODIFIER	silent_mutation	Average:61.339; most accessible tissue: Callus, score: 84.077	N	N	N	N
vg1001913135	T -> A	LOC_Os10g04130.1	upstream_gene_variant ; 17.0bp to feature; MODIFIER	silent_mutation	Average:61.339; most accessible tissue: Callus, score: 84.077	N	N	N	N
vg1001913135	T -> A	LOC_Os10g04120-LOC_Os10g04130	intergenic_region ; MODIFIER	silent_mutation	Average:61.339; most accessible tissue: Callus, score: 84.077	N	N	N	N
vg1001913135	T -> DEL	N	N	silent_mutation	Average:61.339; most accessible tissue: Callus, score: 84.077	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1001913135	2.64E-06	2.63E-06	mr1473_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
vg1001913135	1.20E-06	1.19E-06	mr1630_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
vg1001913135	3.92E-06	3.92E-06	mr1630_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