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Detailed information for vg0403136466:

Variant ID: vg0403136466 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 3136466
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GACATGTAAATATACATATCCAAACGTAAATAAAGCGTAAATACTTATAAAAGAGTCACTTAGTCCTCACACCGAAAAGAAAGCAACAGCAGCGGAAAAA[T/G]
GCGATCTTAGCGGGGTTTTAGCTCCAATCCACAGGTAAAAACTCAACTGGGGTATAAGTCTCAGTCTTCTAACTCCGTCTTCAGCTCAGAAGCACTACAC

Reverse complement sequence

GTGTAGTGCTTCTGAGCTGAAGACGGAGTTAGAAGACTGAGACTTATACCCCAGTTGAGTTTTTACCTGTGGATTGGAGCTAAAACCCCGCTAAGATCGC[A/C]
TTTTTCCGCTGCTGTTGCTTTCTTTTCGGTGTGAGGACTAAGTGACTCTTTTATAAGTATTTACGCTTTATTTACGTTTGGATATGTATATTTACATGTC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	61.60%	7.30%	0.63%	30.43%	NA
All Indica	2759	69.10%	9.90%	0.51%	20.44%	NA
All Japonica	1512	56.90%	4.00%	1.06%	38.10%	NA
Aus	269	11.90%	0.40%	0.00%	87.73%	NA
Indica I	595	97.80%	0.30%	0.00%	1.85%	NA
Indica II	465	74.20%	2.40%	1.29%	22.15%	NA
Indica III	913	45.50%	21.20%	0.22%	33.08%	NA
Indica Intermediate	786	71.90%	8.50%	0.76%	18.83%	NA
Temperate Japonica	767	74.40%	7.30%	0.39%	17.86%	NA
Tropical Japonica	504	31.90%	0.40%	2.38%	65.28%	NA
Japonica Intermediate	241	53.10%	0.80%	0.41%	45.64%	NA
VI/Aromatic	96	55.20%	2.10%	0.00%	42.71%	NA
Intermediate	90	66.70%	10.00%	0.00%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0403136466	T -> DEL	N	N	silent_mutation	Average:19.634; most accessible tissue: Zhenshan97 flag leaf, score: 54.545	N	N	N	N
vg0403136466	T -> G	LOC_Os04g06050.1	downstream_gene_variant ; 2972.0bp to feature; MODIFIER	silent_mutation	Average:19.634; most accessible tissue: Zhenshan97 flag leaf, score: 54.545	N	N	N	N
vg0403136466	T -> G	LOC_Os04g06030-LOC_Os04g06050	intergenic_region ; MODIFIER	silent_mutation	Average:19.634; most accessible tissue: Zhenshan97 flag leaf, score: 54.545	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0403136466	2.34E-06	NA	mr1117_2	Ind_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
vg0403136466	4.47E-06	NA	mr1119_2	Ind_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