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Detailed information for vg1208212661:

Variant ID: vg1208212661 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 8212661
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATGTAGAGCCCCATGCTGCTTGGGAGGTCACTGCAGTGATCCTCACTGGCTCACCTGAGAGGACTTCGTTGGCAGTCACCGCGGGAGGAGATTCTTTCTC[T/C]
GCCGCTTGCCAGAACGCCGCACTCCTCGCCATCGGCACTCTTCACCAGCGCTACCCGGACGAGTTGCAGCACTCGCCCTACCGCTACCACCCTCGTCGCG

Reverse complement sequence

CGCGACGAGGGTGGTAGCGGTAGGGCGAGTGCTGCAACTCGTCCGGGTAGCGCTGGTGAAGAGTGCCGATGGCGAGGAGTGCGGCGTTCTGGCAAGCGGC[A/G]
GAGAAAGAATCTCCTCCCGCGGTGACTGCCAACGAAGTCCTCTCAGGTGAGCCAGTGAGGATCACTGCAGTGACCTCCCAAGCAGCATGGGGCTCTACAT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	85.20%	0.80%	6.39%	7.60%	NA
All Indica	2759	84.80%	1.30%	9.86%	4.02%	NA
All Japonica	1512	81.90%	0.20%	1.79%	16.07%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	87.20%	0.20%	6.55%	6.05%	NA
Indica II	465	80.20%	0.40%	12.47%	6.88%	NA
Indica III	913	84.60%	2.60%	11.61%	1.20%	NA
Indica Intermediate	786	85.90%	1.30%	8.78%	4.07%	NA
Temperate Japonica	767	83.20%	0.10%	1.43%	15.25%	NA
Tropical Japonica	504	86.30%	0.40%	1.59%	11.71%	NA
Japonica Intermediate	241	68.90%	0.00%	3.32%	27.80%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	92.20%	0.00%	2.22%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1208212661	T -> C	LOC_Os12g14400.1	synonymous_variant ; p.Ser149Ser; LOW	synonymous_codon	Average:32.316; most accessible tissue: Zhenshan97 flag leaf, score: 56.722	N	N	N	N
vg1208212661	T -> DEL	LOC_Os12g14400.1	N	frameshift_variant	Average:32.316; most accessible tissue: Zhenshan97 flag leaf, score: 56.722	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1208212661	2.98E-06	4.58E-07	mr1689	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