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Detailed information for vg1206939533:

Variant ID: vg1206939533 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 6939533
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAGGAGGACTTCAGAGTAGGAGGATTTTAGGATGGTGACTATCCAGTTTATCCACCACTATGGGAACCTCGTTGGTGTAGAAGGCTGAGCAGTGGGTAAT[T/C]
CCAACGTACCGAGTCAAAAGCTTTGGAAATGTCGAGTTTGAAGAGCAGCGAGGAGCTTATGTTGCGATGCTAACACCTAACACCTAATTAAGTTCCGGAC

Reverse complement sequence

GTCCGGAACTTAATTAGGTGTTAGGTGTTAGCATCGCAACATAAGCTCCTCGCTGCTCTTCAAACTCGACATTTCCAAAGCTTTTGACTCGGTACGTTGG[A/G]
ATTACCCACTGCTCAGCCTTCTACACCAACGAGGTTCCCATAGTGGTGGATAAACTGGATAGTCACCATCCTAAAATCCTCCTACTCTGAAGTCCTCCTA

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	63.20%	36.40%	0.06%	0.28%	NA
All Indica	2759	93.50%	6.00%	0.07%	0.40%	NA
All Japonica	1512	6.80%	93.10%	0.00%	0.13%	NA
Aus	269	72.10%	27.90%	0.00%	0.00%	NA
Indica I	595	97.80%	1.50%	0.17%	0.50%	NA
Indica II	465	96.10%	3.70%	0.00%	0.22%	NA
Indica III	913	91.60%	8.00%	0.00%	0.44%	NA
Indica Intermediate	786	91.10%	8.40%	0.13%	0.38%	NA
Temperate Japonica	767	10.30%	89.70%	0.00%	0.00%	NA
Tropical Japonica	504	3.60%	96.00%	0.00%	0.40%	NA
Japonica Intermediate	241	2.50%	97.50%	0.00%	0.00%	NA
VI/Aromatic	96	77.10%	22.90%	0.00%	0.00%	NA
Intermediate	90	40.00%	58.90%	1.11%	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
vg1206939533	T -> C	LOC_Os12g12590.1	downstream_gene_variant ; 2462.0bp to feature; MODIFIER	silent_mutation	Average:55.945; most accessible tissue: Zhenshan97 young leaf, score: 75.397	N	N	N	N
vg1206939533	T -> C	LOC_Os12g12590-LOC_Os12g12600	intergenic_region ; MODIFIER	silent_mutation	Average:55.945; most accessible tissue: Zhenshan97 young leaf, score: 75.397	N	N	N	N
vg1206939533	T -> DEL	N	N	silent_mutation	Average:55.945; most accessible tissue: Zhenshan97 young leaf, score: 75.397	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1206939533	NA	2.51E-26	mr1024	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
vg1206939533	NA	1.75E-12	mr1940	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
vg1206939533	NA	8.79E-12	mr1666_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
vg1206939533	7.10E-07	NA	mr1855_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
vg1206939533	NA	1.06E-20	mr1922_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
vg1206939533	NA	7.75E-09	mr1940_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