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Detailed information for vg0331809182:

Variant ID: vg0331809182 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 31809182
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTCCCGTGTAGTACAGTAATATTTACTCCGGCTAGGCTTACCTGCTTGTGCATCTTCACAGGTTTTGATTCTCCGGTTCTCTTAGTTTCCTGGCAACTTT[G/A]
AAAAGAGCGGAACACTAGGGTTTTCAATTTTTTTTCTTTCACCGGTCTCGATGGTTATGTAGTCCATTCACTAGCAGGGTTGTCTCTGGTCTCTCCTTGG

Reverse complement sequence

CCAAGGAGAGACCAGAGACAACCCTGCTAGTGAATGGACTACATAACCATCGAGACCGGTGAAAGAAAAAAAATTGAAAACCCTAGTGTTCCGCTCTTTT[C/T]
AAAGTTGCCAGGAAACTAAGAGAACCGGAGAATCAAAACCTGTGAAGATGCACAAGCAGGTAAGCCTAGCCGGAGTAAATATTACTGTACTACACGGGAA

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	96.10%	3.50%	0.40%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	88.80%	10.10%	1.19%	0.00%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	67.30%	29.20%	3.57%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	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
vg0331809182	G -> A	LOC_Os03g55870.1	downstream_gene_variant ; 4999.0bp to feature; MODIFIER	silent_mutation	Average:62.139; most accessible tissue: Callus, score: 80.987	N	N	N	N
vg0331809182	G -> A	LOC_Os03g55870-LOC_Os03g55874	intergenic_region ; MODIFIER	silent_mutation	Average:62.139; most accessible tissue: Callus, score: 80.987	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0331809182	1.81E-07	NA	mr1134_2	Jap_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
vg0331809182	1.20E-06	NA	mr1504_2	Jap_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