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Detailed information for vg1216759163:

Variant ID: vg1216759163 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 16759163
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATCAGGGCAAGCGCCTGAGTAGCTTCCTCTTCCATTGGAAGTGAGTTCCAAGTGTCTTGATAAACTGGAGGAAGACAGGAGTACTCGGGGAGTGCAGGCT[T/C]
GGGGTTTTGTACATAGAACCAATTTGCATGCCAGCCTTTGTTTGAGGTTTTGAAGGGCATGGAGAAATACTTTTGGCTCAGAGTTCCCCTCAGTTGAAAT

Reverse complement sequence

ATTTCAACTGAGGGGAACTCTGAGCCAAAAGTATTTCTCCATGCCCTTCAAAACCTCAAACAAAGGCTGGCATGCAAATTGGTTCTATGTACAAAACCCC[A/G]
AGCCTGCACTCCCCGAGTACTCCTGTCTTCCTCCAGTTTATCAAGACACTTGGAACTCACTTCCAATGGAAGAGGAAGCTACTCAGGCGCTTGCCCTGAT

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	40.10%	8.00%	1.04%	50.80%	NA
All Indica	2759	22.90%	0.70%	1.38%	75.03%	NA
All Japonica	1512	76.00%	17.50%	0.20%	6.28%	NA
Aus	269	23.00%	0.00%	2.97%	73.98%	NA
Indica I	595	48.40%	1.00%	2.86%	47.73%	NA
Indica II	465	25.80%	0.20%	0.86%	73.12%	NA
Indica III	913	2.70%	0.40%	0.22%	96.60%	NA
Indica Intermediate	786	25.20%	1.10%	1.91%	71.76%	NA
Temperate Japonica	767	96.20%	0.30%	0.00%	3.52%	NA
Tropical Japonica	504	42.70%	46.80%	0.40%	10.12%	NA
Japonica Intermediate	241	81.30%	11.20%	0.41%	7.05%	NA
VI/Aromatic	96	9.40%	79.20%	0.00%	11.46%	NA
Intermediate	90	51.10%	20.00%	0.00%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1216759163	T -> C	LOC_Os12g28340.1	missense_variant ; p.Lys155Glu; MODERATE	nonsynonymous_codon ; K155E	Average:10.067; most accessible tissue: Callus, score: 30.309	unknown	unknown	TOLERATED	1.00
vg1216759163	T -> DEL	LOC_Os12g28340.1	N	frameshift_variant	Average:10.067; most accessible tissue: Callus, score: 30.309	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1216759163	4.87E-06	NA	mr1296	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