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Detailed information for vg0313141983:

Variant ID: vg0313141983 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 13141983
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACGGTGGCGCACGCCTTCTTCAAGATGCATCCGTCGCCAGCCGTGCGCACGTTTGGGTTTCTCTGATCTCGAGAGGCGGCTGCGATGATCGTCGACGGTG[C/A]
ACGAGTGGAATTGGTGTGTAATTTATTGCACATGGAAAATTGCTGGACTCATTTATATTTTTTAGACTAGATGTATGCATGCAGTTTTAATTTTGTATGT

Reverse complement sequence

ACATACAAAATTAAAACTGCATGCATACATCTAGTCTAAAAAATATAAATGAGTCCAGCAATTTTCCATGTGCAATAAATTACACACCAATTCCACTCGT[G/T]
CACCGTCGACGATCATCGCAGCCGCCTCTCGAGATCAGAGAAACCCAAACGTGCGCACGGCTGGCGACGGATGCATCTTGAAGAAGGCGTGCGCCACCGT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	94.40%	5.60%	0.00%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	82.70%	17.30%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	68.10%	31.90%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	92.90%	7.10%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	3.30%	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
vg0313141983	C -> A	LOC_Os03g22740.1	upstream_gene_variant ; 4803.0bp to feature; MODIFIER	silent_mutation	Average:69.705; most accessible tissue: Callus, score: 84.493	N	N	N	N
vg0313141983	C -> A	LOC_Os03g22750.1	downstream_gene_variant ; 35.0bp to feature; MODIFIER	silent_mutation	Average:69.705; most accessible tissue: Callus, score: 84.493	N	N	N	N
vg0313141983	C -> A	LOC_Os03g22750-LOC_Os03g22760	intergenic_region ; MODIFIER	silent_mutation	Average:69.705; most accessible tissue: Callus, score: 84.493	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0313141983	2.52E-06	NA	mr1137	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0313141983	1.06E-07	NA	mr1617	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