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Detailed information for vg1203045015:

Variant ID: vg1203045015 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 3045015
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCAGCGCACCCGAAACAGCCACCAACTGGCGGCGCTAATGGCGAAAACCCTGAACAGCGGGAATCGCCTCATCGAGCCACCCCTCCACCTTGAGGCACCG[G/A]
CGATCTCCGCAATCACCTGAATGGCTACCGAGAGGCGCGACGCGCACGAGACAACGAGAACCGTTCCCGACATCGCGTCTCTTCAGGACGTCACGATAAC

Reverse complement sequence

GTTATCGTGACGTCCTGAAGAGACGCGATGTCGGGAACGGTTCTCGTTGTCTCGTGCGCGTCGCGCCTCTCGGTAGCCATTCAGGTGATTGCGGAGATCG[C/T]
CGGTGCCTCAAGGTGGAGGGGTGGCTCGATGAGGCGATTCCCGCTGTTCAGGGTTTTCGCCATTAGCGCCGCCAGTTGGTGGCTGTTTCGGGTGCGCTGC

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	93.40%	5.10%	1.46%	0.00%	NA
All Indica	2759	99.40%	0.10%	0.54%	0.00%	NA
All Japonica	1512	80.80%	15.60%	3.57%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.50%	0.00%	1.51%	0.00%	NA
Indica II	465	99.40%	0.00%	0.65%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.40%	0.30%	0.38%	0.00%	NA
Temperate Japonica	767	67.30%	26.50%	6.26%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	84.20%	13.30%	2.49%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	2.20%	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
vg1203045015	G -> A	LOC_Os12g06360.1	upstream_gene_variant ; 2333.0bp to feature; MODIFIER	silent_mutation	Average:52.951; most accessible tissue: Minghui63 young leaf, score: 68.07	N	N	N	N
vg1203045015	G -> A	LOC_Os12g06350.1	intron_variant ; MODIFIER	silent_mutation	Average:52.951; most accessible tissue: Minghui63 young leaf, score: 68.07	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1203045015	NA	2.50E-06	mr1582_2	Jap_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
vg1203045015	3.29E-06	NA	mr1778_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