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Detailed information for vg1123973539:

Variant ID: vg1123973539 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 23973539
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCTCCTTCTCTCTTTATCGTCATTTGGATTTTAAAAATCGAATATAATGATCGTCGGTGTTCACTTTTAACTTTGTAGAAGTCCCACCAAGCCATAAGCA[A/G]
GTTAGCCATTATACTCCTAAACGGCCCATCCGATGTCTTCCCTTTTAATTGTCATTGATATTTTAAAATTCGAACGTGATTCTCATTATGGTTTATTTTT

Reverse complement sequence

AAAAATAAACCATAATGAGAATCACGTTCGAATTTTAAAATATCAATGACAATTAAAAGGGAAGACATCGGATGGGCCGTTTAGGAGTATAATGGCTAAC[T/C]
TGCTTATGGCTTGGTGGGACTTCTACAAAGTTAAAAGTGAACACCGACGATCATTATATTCGATTTTTAAAATCCAAATGACGATAAAGAGAGAAGGAGA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	72.60%	6.50%	1.40%	19.51%	NA
All Indica	2759	68.20%	2.80%	1.20%	27.84%	NA
All Japonica	1512	84.30%	13.20%	1.65%	0.86%	NA
Aus	269	51.70%	4.80%	0.74%	42.75%	NA
Indica I	595	76.30%	0.50%	0.17%	23.03%	NA
Indica II	465	70.10%	1.90%	1.08%	26.88%	NA
Indica III	913	58.90%	6.00%	1.75%	33.30%	NA
Indica Intermediate	786	71.80%	1.10%	1.40%	25.70%	NA
Temperate Japonica	767	84.20%	12.30%	2.22%	1.30%	NA
Tropical Japonica	504	88.30%	10.90%	0.40%	0.40%	NA
Japonica Intermediate	241	76.30%	20.70%	2.49%	0.41%	NA
VI/Aromatic	96	79.20%	10.40%	3.12%	7.29%	NA
Intermediate	90	67.80%	7.80%	3.33%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1123973539	A -> DEL	N	N	silent_mutation	Average:19.769; most accessible tissue: Callus, score: 55.254	N	N	N	N
vg1123973539	A -> G	LOC_Os11g40200.1	upstream_gene_variant ; 3248.0bp to feature; MODIFIER	silent_mutation	Average:19.769; most accessible tissue: Callus, score: 55.254	N	N	N	N
vg1123973539	A -> G	LOC_Os11g40180.1	downstream_gene_variant ; 4642.0bp to feature; MODIFIER	silent_mutation	Average:19.769; most accessible tissue: Callus, score: 55.254	N	N	N	N
vg1123973539	A -> G	LOC_Os11g40180-LOC_Os11g40200	intergenic_region ; MODIFIER	silent_mutation	Average:19.769; most accessible tissue: Callus, score: 55.254	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1123973539	2.60E-08	NA	mr1024_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