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Detailed information for vg1208195076:

Variant ID: vg1208195076 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 8195076
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.47, G: 0.37, T: 0.16, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:

GCTTCCATCTTTATGATACTCTAATCATGTTTATGTAATTCATCGAGTTATCATATATCTTACATAATCTCTGGCAATATCATTATCTAACCTACAATCG[A/G]
CTAACATCTGTCAGTAGAGGGCAGCCGATTAGGTTAGATTTTGATGTTGATTTAGATTATATAAGATCTCCACCACTCTATGAAACTTCCAGCGGCTTGA

Reverse complement sequence

TCAAGCCGCTGGAAGTTTCATAGAGTGGTGGAGATCTTATATAATCTAAATCAACATCAAAATCTAACCTAATCGGCTGCCCTCTACTGACAGATGTTAG[T/C]
CGATTGTAGGTTAGATAATGATATTGCCAGAGATTATGTAAGATATATGATAACTCGATGAATTACATAAACATGATTAGAGTATCATAAAGATGGAAGC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	48.10%	26.40%	0.47%	25.03%	NA
All Indica	2759	49.70%	37.90%	0.43%	11.96%	NA
All Japonica	1512	51.20%	4.40%	0.40%	44.05%	NA
Aus	269	20.40%	30.10%	0.37%	49.07%	NA
Indica I	595	37.60%	46.90%	0.50%	14.96%	NA
Indica II	465	42.40%	51.20%	0.22%	6.24%	NA
Indica III	913	60.20%	27.30%	0.44%	12.05%	NA
Indica Intermediate	786	51.00%	35.50%	0.51%	12.98%	NA
Temperate Japonica	767	74.30%	6.30%	0.26%	19.17%	NA
Tropical Japonica	504	23.00%	2.00%	0.40%	74.60%	NA
Japonica Intermediate	241	36.50%	3.30%	0.83%	59.34%	NA
VI/Aromatic	96	24.00%	36.50%	2.08%	37.50%	NA
Intermediate	90	56.70%	21.10%	1.11%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1208195076	A -> DEL	N	N	silent_mutation	Average:30.059; most accessible tissue: Zhenshan97 flag leaf, score: 55.285	N	N	N	N
vg1208195076	A -> G	LOC_Os12g14374.1	intron_variant ; MODIFIER	silent_mutation	Average:30.059; most accessible tissue: Zhenshan97 flag leaf, score: 55.285	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1208195076	NA	1.44E-08	mr1425	Ind_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
vg1208195076	NA	1.17E-06	mr1577	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
vg1208195076	NA	6.20E-11	mr1581	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
vg1208195076	NA	6.74E-08	mr1864_2	Ind_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