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Detailed information for vg0323551151:

Variant ID: vg0323551151 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 23551151
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTTCACATCATTTTCACATTATTTAAGCATATATGTCTACTATTTTTATAATGTACTGTATAACATGTATTTATCCACATATCCCGCGATAAAGCACGGA[G/A]
TATCAATTAGTTATTATTATAAACACACACGTAGATGGTGGTTTAGTTTTGGTTGTGGTCAATTCGAAAAAAAAATCGTAATTGGATCGAGCCAAATAAA

Reverse complement sequence

TTTATTTGGCTCGATCCAATTACGATTTTTTTTTCGAATTGACCACAACCAAAACTAAACCACCATCTACGTGTGTGTTTATAATAATAACTAATTGATA[C/T]
TCCGTGCTTTATCGCGGGATATGTGGATAAATACATGTTATACAGTACATTATAAAAATAGTAGACATATATGCTTAAATAATGTGAAAATGATGTGAAC

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	89.80%	5.10%	1.80%	3.28%	NA
All Indica	2759	82.90%	8.60%	3.04%	5.47%	NA
All Japonica	1512	99.70%	0.20%	0.00%	0.07%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	92.90%	2.00%	4.71%	0.34%	NA
Indica II	465	89.90%	0.90%	2.15%	7.10%	NA
Indica III	913	73.40%	14.70%	1.75%	10.19%	NA
Indica Intermediate	786	82.30%	10.90%	3.82%	2.93%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.00%	0.20%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	2.20%	1.11%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0323551151	G -> A	LOC_Os03g42320.1	upstream_gene_variant ; 3483.0bp to feature; MODIFIER	silent_mutation	Average:21.156; most accessible tissue: Callus, score: 48.596	N	N	N	N
vg0323551151	G -> A	LOC_Os03g42334.1	upstream_gene_variant ; 4214.0bp to feature; MODIFIER	silent_mutation	Average:21.156; most accessible tissue: Callus, score: 48.596	N	N	N	N
vg0323551151	G -> A	LOC_Os03g42320-LOC_Os03g42334	intergenic_region ; MODIFIER	silent_mutation	Average:21.156; most accessible tissue: Callus, score: 48.596	N	N	N	N
vg0323551151	G -> DEL	N	N	silent_mutation	Average:21.156; most accessible tissue: Callus, score: 48.596	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0323551151	1.31E-06	NA	mr1037_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