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Detailed information for vg0612526873:

Variant ID: vg0612526873 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 12526873
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTCCTATTATTTCAAAGCCTAACTAGGCGCGCAGCGGTGAGTGCGAGCTGCTTTCAAGAAATGCTGGAAAAGAGCCAGTAACGCTATCAGTGAATAGAGC[T/C]
GGTGTAAAGTCCGGCTAAAGTACCATACAGCCCCACAGGTTTAGCCACACATTCACAGAGCATCTAATCCATCTTTTCCCATGCCAAGGAAAAACAAAAA

Reverse complement sequence

TTTTTGTTTTTCCTTGGCATGGGAAAAGATGGATTAGATGCTCTGTGAATGTGTGGCTAAACCTGTGGGGCTGTATGGTACTTTAGCCGGACTTTACACC[A/G]
GCTCTATTCACTGATAGCGTTACTGGCTCTTTTCCAGCATTTCTTGAAAGCAGCTCGCACTCACCGCTGCGCGCCTAGTTAGGCTTTGAAATAATAGGAA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	66.90%	33.00%	0.11%	0.00%	NA
All Indica	2759	97.00%	2.80%	0.14%	0.00%	NA
All Japonica	1512	11.10%	88.80%	0.07%	0.00%	NA
Aus	269	83.30%	16.70%	0.00%	0.00%	NA
Indica I	595	96.60%	3.20%	0.17%	0.00%	NA
Indica II	465	97.20%	2.60%	0.22%	0.00%	NA
Indica III	913	99.50%	0.40%	0.11%	0.00%	NA
Indica Intermediate	786	94.40%	5.50%	0.13%	0.00%	NA
Temperate Japonica	767	3.30%	96.60%	0.13%	0.00%	NA
Tropical Japonica	504	23.80%	76.20%	0.00%	0.00%	NA
Japonica Intermediate	241	9.50%	90.50%	0.00%	0.00%	NA
VI/Aromatic	96	42.70%	57.30%	0.00%	0.00%	NA
Intermediate	90	57.80%	42.20%	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
vg0612526873	T -> C	LOC_Os06g21680-LOC_Os06g21690	intergenic_region ; MODIFIER	silent_mutation	Average:40.955; most accessible tissue: Minghui63 flag leaf, score: 73.752	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0612526873	NA	9.11E-21	mr1588	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
vg0612526873	1.61E-06	NA	mr1201_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
vg0612526873	1.38E-06	NA	mr1219_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
vg0612526873	NA	2.91E-15	mr1686_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
vg0612526873	NA	9.89E-07	mr1915_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