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Detailed information for vg0207801637:

Variant ID: vg0207801637 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 7801637
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCAAATCGGAGTTGGCGTGAAGACGCTAGGTCTGCTTAAAGTCATTGCTGTCTCCGGAGGCCGAACTGTATTCCAAAACTTATTGGACTTTAATATGTTA[T/G]
AGATACTCCATTCACTCGATGTATTCTTTGACAATATTTTATATTTCTTATGCTTCGTTGTATGCATATACTTGATGGTCACATCACGTAGGCAACACCC

Reverse complement sequence

GGGTGTTGCCTACGTGATGTGACCATCAAGTATATGCATACAACGAAGCATAAGAAATATAAAATATTGTCAAAGAATACATCGAGTGAATGGAGTATCT[A/C]
TAACATATTAAAGTCCAATAAGTTTTGGAATACAGTTCGGCCTCCGGAGACAGCAATGACTTTAAGCAGACCTAGCGTCTTCACGCCAACTCCGATTTGG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	94.90%	3.10%	1.97%	0.00%	NA
All Indica	2759	91.70%	5.00%	3.23%	0.00%	NA
All Japonica	1512	99.50%	0.30%	0.13%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	90.60%	2.90%	6.55%	0.00%	NA
Indica II	465	77.40%	18.30%	4.30%	0.00%	NA
Indica III	913	99.80%	0.00%	0.22%	0.00%	NA
Indica Intermediate	786	91.70%	4.70%	3.56%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	98.80%	0.80%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	3.30%	2.22%	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
vg0207801637	T -> G	LOC_Os02g14230.1	upstream_gene_variant ; 3378.0bp to feature; MODIFIER	silent_mutation	Average:48.876; most accessible tissue: Minghui63 panicle, score: 66.554	N	N	N	N
vg0207801637	T -> G	LOC_Os02g14230-LOC_Os02g14240	intergenic_region ; MODIFIER	silent_mutation	Average:48.876; most accessible tissue: Minghui63 panicle, score: 66.554	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0207801637	NA	5.85E-06	mr1909	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