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Detailed information for vg0802104427:

Variant ID: vg0802104427 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 2104427
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAAACATAGGCCATTTTAGGCGTTCACAAATCAAACTCCAACCACCTCGATCGGTAATTCAGCAAGCTTCTCGTTCTTGCATTACCAGGAACCTGGTTTG[G/A]
CTCCAACCGACCCCGCCCTGGCGTTCCCAACTATTGGCATGCGAGGTTTCCCTGAACCGACTAGTTACTTAGCCAGGGTGTCCCATTCCACCTTGTGGTT

Reverse complement sequence

AACCACAAGGTGGAATGGGACACCCTGGCTAAGTAACTAGTCGGTTCAGGGAAACCTCGCATGCCAATAGTTGGGAACGCCAGGGCGGGGTCGGTTGGAG[C/T]
CAAACCAGGTTCCTGGTAATGCAAGAACGAGAAGCTTGCTGAATTACCGATCGAGGTGGTTGGAGTTTGATTTGTGAACGCCTAAAATGGCCTATGTTTA

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	46.80%	0.10%	26.32%	26.72%	NA
All Indica	2759	14.40%	0.20%	41.14%	44.29%	NA
All Japonica	1512	98.60%	0.00%	0.53%	0.86%	NA
Aus	269	65.10%	0.00%	30.86%	4.09%	NA
Indica I	595	17.30%	0.20%	13.61%	68.91%	NA
Indica II	465	6.00%	0.00%	30.75%	63.23%	NA
Indica III	913	17.10%	0.00%	66.37%	16.54%	NA
Indica Intermediate	786	14.00%	0.50%	38.80%	46.69%	NA
Temperate Japonica	767	98.40%	0.00%	0.65%	0.91%	NA
Tropical Japonica	504	99.00%	0.00%	0.40%	0.60%	NA
Japonica Intermediate	241	98.30%	0.00%	0.41%	1.24%	NA
VI/Aromatic	96	96.90%	0.00%	2.08%	1.04%	NA
Intermediate	90	64.40%	0.00%	17.78%	17.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0802104427	G -> A	LOC_Os08g04300.1	upstream_gene_variant ; 3873.0bp to feature; MODIFIER	silent_mutation	Average:11.475; most accessible tissue: Minghui63 young leaf, score: 20.156	N	N	N	N
vg0802104427	G -> A	LOC_Os08g04290.1	downstream_gene_variant ; 3823.0bp to feature; MODIFIER	silent_mutation	Average:11.475; most accessible tissue: Minghui63 young leaf, score: 20.156	N	N	N	N
vg0802104427	G -> A	LOC_Os08g04290-LOC_Os08g04300	intergenic_region ; MODIFIER	silent_mutation	Average:11.475; most accessible tissue: Minghui63 young leaf, score: 20.156	N	N	N	N
vg0802104427	G -> DEL	N	N	silent_mutation	Average:11.475; most accessible tissue: Minghui63 young leaf, score: 20.156	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0802104427	6.83E-06	NA	mr1881	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