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Detailed information for vg0104901845:

Variant ID: vg0104901845 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 4901845
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AACGTTTAACCATTTATCTTATTTAAAAGATTATAAAATTATTATTTATTTTATTTGTGACTTGATTTATTATCAAAAGTGCTTCAAATATGACTGTACT[G/A]
TTTTTTAAATAAAATAAATGGCCAAACGTGGTAAGTAAAAGGTTAAAATGACATCTAATTAGGACGTCTGGAGTACTAACATGCATATATGACCTGAGAC

Reverse complement sequence

GTCTCAGGTCATATATGCATGTTAGTACTCCAGACGTCCTAATTAGATGTCATTTTAACCTTTTACTTACCACGTTTGGCCATTTATTTTATTTAAAAAA[C/T]
AGTACAGTCATATTTGAAGCACTTTTGATAATAAATCAAGTCACAAATAAAATAAATAATAATTTTATAATCTTTTAAATAAGATAAATGGTTAAACGTT

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	95.70%	4.20%	0.08%	0.00%	NA
All Indica	2759	99.10%	0.90%	0.00%	0.00%	NA
All Japonica	1512	96.60%	3.10%	0.26%	0.00%	NA
Aus	269	63.90%	36.10%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	98.70%	1.30%	0.00%	0.00%	NA
Indica Intermediate	786	98.70%	1.30%	0.00%	0.00%	NA
Temperate Japonica	767	99.50%	0.40%	0.13%	0.00%	NA
Tropical Japonica	504	94.00%	5.40%	0.60%	0.00%	NA
Japonica Intermediate	241	92.90%	7.10%	0.00%	0.00%	NA
VI/Aromatic	96	77.10%	22.90%	0.00%	0.00%	NA
Intermediate	90	92.20%	7.80%	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
vg0104901845	G -> A	LOC_Os01g09570.1	upstream_gene_variant ; 3656.0bp to feature; MODIFIER	silent_mutation	Average:74.496; most accessible tissue: Zhenshan97 root, score: 88.158	N	N	N	N
vg0104901845	G -> A	LOC_Os01g09560.1	downstream_gene_variant ; 4969.0bp to feature; MODIFIER	silent_mutation	Average:74.496; most accessible tissue: Zhenshan97 root, score: 88.158	N	N	N	N
vg0104901845	G -> A	LOC_Os01g09560-LOC_Os01g09570	intergenic_region ; MODIFIER	silent_mutation	Average:74.496; most accessible tissue: Zhenshan97 root, score: 88.158	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0104901845	4.91E-07	NA	mr1240	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