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Detailed information for vg1210199420:

Variant ID: vg1210199420 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 10199420
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCCTTCACAGGGTCGGTCAGACCGCAGGTATATGGGCGGTCTGACCGTCAGGGTTAGAGTCCGAGTCTGTTTTTGTCGGGTCTCGGGTTTCCTTGCTCGG[G/A]
AAGACATGTTTCGTGTTTCATTTGGTTTCTATCCCGAGTTGGGCATGGAGAAGGGCTTGTAGAGGGCAAGACCAACCCCTATTTAAGGGACAAGGCCGAT

Reverse complement sequence

ATCGGCCTTGTCCCTTAAATAGGGGTTGGTCTTGCCCTCTACAAGCCCTTCTCCATGCCCAACTCGGGATAGAAACCAAATGAAACACGAAACATGTCTT[C/T]
CCGAGCAAGGAAACCCGAGACCCGACAAAAACAGACTCGGACTCTAACCCTGACGGTCAGACCGCCCATATACCTGCGGTCTGACCGACCCTGTGAAGGA

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	93.30%	6.20%	0.47%	0.00%	NA
All Indica	2759	96.50%	3.20%	0.25%	0.00%	NA
All Japonica	1512	98.10%	1.90%	0.00%	0.00%	NA
Aus	269	47.20%	47.60%	5.20%	0.00%	NA
Indica I	595	94.10%	5.90%	0.00%	0.00%	NA
Indica II	465	99.10%	0.90%	0.00%	0.00%	NA
Indica III	913	97.20%	2.40%	0.44%	0.00%	NA
Indica Intermediate	786	96.10%	3.60%	0.38%	0.00%	NA
Temperate Japonica	767	96.90%	3.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	54.20%	44.80%	1.04%	0.00%	NA
Intermediate	90	93.30%	6.70%	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
vg1210199420	G -> A	LOC_Os12g17804.1	upstream_gene_variant ; 3007.0bp to feature; MODIFIER	silent_mutation	Average:37.684; most accessible tissue: Minghui63 flag leaf, score: 68.675	N	N	N	N
vg1210199420	G -> A	LOC_Os12g17810.1	downstream_gene_variant ; 1140.0bp to feature; MODIFIER	silent_mutation	Average:37.684; most accessible tissue: Minghui63 flag leaf, score: 68.675	N	N	N	N
vg1210199420	G -> A	LOC_Os12g17804-LOC_Os12g17810	intergenic_region ; MODIFIER	silent_mutation	Average:37.684; most accessible tissue: Minghui63 flag leaf, score: 68.675	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1210199420	NA	2.10E-06	mr1029	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
vg1210199420	3.29E-06	NA	mr1892	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
vg1210199420	NA	1.02E-06	mr1567_2	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