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Detailed information for vg1226733008:

Variant ID: vg1226733008 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 26733008
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAGCTTGACCAGGGCTACACCTAATCTTCCACACCATCAGCATCACTGTAGAACTCCTCCTCTGATGAATGATTGCTAGGTGAGTATATGACATACTCAG[C/A]
AAGCCACGCAACAAATATGCAAGTGCACAGGATAACAAAGGATGGCATAGTAGGGTTTCATTTGCATAAACAGCATTTAATAAACATTTCAGAATTTAAT

Reverse complement sequence

ATTAAATTCTGAAATGTTTATTAAATGCTGTTTATGCAAATGAAACCCTACTATGCCATCCTTTGTTATCCTGTGCACTTGCATATTTGTTGCGTGGCTT[G/T]
CTGAGTATGTCATATACTCACCTAGCAATCATTCATCAGAGGAGGAGTTCTACAGTGATGCTGATGGTGTGGAAGATTAGGTGTAGCCCTGGTCAAGCTG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	98.30%	1.20%	0.51%	0.00%	NA
All Indica	2759	99.90%	0.00%	0.07%	0.00%	NA
All Japonica	1512	95.00%	3.60%	1.39%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.00%	0.25%	0.00%	NA
Temperate Japonica	767	98.40%	1.40%	0.13%	0.00%	NA
Tropical Japonica	504	89.30%	7.50%	3.17%	0.00%	NA
Japonica Intermediate	241	95.90%	2.50%	1.66%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	1.10%	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
vg1226733008	C -> A	LOC_Os12g43034.1	upstream_gene_variant ; 1369.0bp to feature; MODIFIER	silent_mutation	Average:33.292; most accessible tissue: Zhenshan97 flag leaf, score: 73.119	N	N	N	N
vg1226733008	C -> A	LOC_Os12g43050.1	downstream_gene_variant ; 2721.0bp to feature; MODIFIER	silent_mutation	Average:33.292; most accessible tissue: Zhenshan97 flag leaf, score: 73.119	N	N	N	N
vg1226733008	C -> A	LOC_Os12g43034-LOC_Os12g43050	intergenic_region ; MODIFIER	silent_mutation	Average:33.292; most accessible tissue: Zhenshan97 flag leaf, score: 73.119	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1226733008	3.87E-07	3.21E-08	mr1871	Jap_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
vg1226733008	NA	8.67E-08	mr1951	Jap_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
vg1226733008	1.99E-06	NA	mr1871_2	Jap_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