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Detailed information for vg0401915452:

Variant ID: vg0401915452 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 1915452
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGCATACGGGCGGAATCGATCTTCACATGCGGTTGGCCGGCCCGCATGTCGCAGCCGTATGCGAAGATATATTTTCCCATGCGGTTGACCTAAGAAGATC[G/A]
CATGCGAAGATCTATTTTCGCATGCGGGCGTCTTAAGTAGACCGCATGCGAAATTCAATTTCCGAATAGCTAAAATAATATTTATTCTAGCATTTTGGTG

Reverse complement sequence

CACCAAAATGCTAGAATAAATATTATTTTAGCTATTCGGAAATTGAATTTCGCATGCGGTCTACTTAAGACGCCCGCATGCGAAAATAGATCTTCGCATG[C/T]
GATCTTCTTAGGTCAACCGCATGGGAAAATATATCTTCGCATACGGCTGCGACATGCGGGCCGGCCAACCGCATGTGAAGATCGATTCCGCCCGTATGCA

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	48.70%	0.10%	12.29%	38.89%	NA
All Indica	2759	47.40%	0.20%	8.19%	44.22%	NA
All Japonica	1512	53.30%	0.00%	10.65%	36.04%	NA
Aus	269	49.40%	0.00%	44.61%	5.95%	NA
Indica I	595	22.90%	0.30%	2.69%	74.12%	NA
Indica II	465	40.60%	0.00%	1.94%	57.42%	NA
Indica III	913	73.10%	0.00%	10.51%	16.43%	NA
Indica Intermediate	786	40.10%	0.50%	13.36%	46.06%	NA
Temperate Japonica	767	62.50%	0.00%	6.65%	30.90%	NA
Tropical Japonica	504	48.00%	0.00%	14.29%	37.70%	NA
Japonica Intermediate	241	35.30%	0.00%	15.77%	48.96%	NA
VI/Aromatic	96	9.40%	0.00%	68.75%	21.88%	NA
Intermediate	90	51.10%	0.00%	8.89%	40.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0401915452	G -> DEL	N	N	silent_mutation	Average:46.321; most accessible tissue: Zhenshan97 panicle, score: 63.607	N	N	N	N
vg0401915452	G -> A	LOC_Os04g04150.1	upstream_gene_variant ; 2974.0bp to feature; MODIFIER	silent_mutation	Average:46.321; most accessible tissue: Zhenshan97 panicle, score: 63.607	N	N	N	N
vg0401915452	G -> A	LOC_Os04g04140.1	downstream_gene_variant ; 306.0bp to feature; MODIFIER	silent_mutation	Average:46.321; most accessible tissue: Zhenshan97 panicle, score: 63.607	N	N	N	N
vg0401915452	G -> A	LOC_Os04g04130-LOC_Os04g04140	intergenic_region ; MODIFIER	silent_mutation	Average:46.321; most accessible tissue: Zhenshan97 panicle, score: 63.607	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0401915452	6.80E-08	5.87E-08	mr1798_2	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