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Detailed information for vg1216931811:

Variant ID: vg1216931811 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 16931811
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATATCTGCCGAATATCCCTTTGATAAATTTGATGGCGTTGTCGGCCTTAATTTCCCCCGTGGGCGTTGCTTCAATCCACTTGGTGAACTTGTCGATCGCC[A/C]
CGAATAGGAACCTGTAGCCGCCCTGTCCTCGTGGGAATGGTCCGAGTATGTCGAGCCCCCAGCACGAGAACGGCCAGGTAAGAGGGATAGTCTAGAGCGC

Reverse complement sequence

GCGCTCTAGACTATCCCTCTTACCTGGCCGTTCTCGTGCTGGGGGCTCGACATACTCGGACCATTCCCACGAGGACAGGGCGGCTACAGGTTCCTATTCG[T/G]
GGCGATCGACAAGTTCACCAAGTGGATTGAAGCAACGCCCACGGGGGAAATTAAGGCCGACAACGCCATCAAATTTATCAAAGGGATATTCGGCAGATAT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	61.10%	1.50%	3.34%	34.09%	NA
All Indica	2759	55.30%	0.60%	3.30%	40.81%	NA
All Japonica	1512	73.90%	1.50%	2.51%	22.16%	NA
Aus	269	56.90%	1.50%	3.35%	38.29%	NA
Indica I	595	40.30%	0.20%	3.53%	55.97%	NA
Indica II	465	61.90%	0.00%	3.23%	34.84%	NA
Indica III	913	62.70%	0.20%	3.72%	33.41%	NA
Indica Intermediate	786	54.20%	1.70%	2.67%	41.48%	NA
Temperate Japonica	767	89.80%	1.60%	2.74%	5.87%	NA
Tropical Japonica	504	47.40%	0.00%	2.38%	50.20%	NA
Japonica Intermediate	241	78.40%	4.10%	2.07%	15.35%	NA
VI/Aromatic	96	40.60%	27.10%	14.58%	17.71%	NA
Intermediate	90	57.80%	2.20%	6.67%	33.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1216931811	A -> C	LOC_Os12g28630.1	upstream_gene_variant ; 2752.0bp to feature; MODIFIER	silent_mutation	Average:14.787; most accessible tissue: Callus, score: 42.051	N	N	N	N
vg1216931811	A -> C	LOC_Os12g28620.1	downstream_gene_variant ; 4859.0bp to feature; MODIFIER	silent_mutation	Average:14.787; most accessible tissue: Callus, score: 42.051	N	N	N	N
vg1216931811	A -> C	LOC_Os12g28640.1	intron_variant ; MODIFIER	silent_mutation	Average:14.787; most accessible tissue: Callus, score: 42.051	N	N	N	N
vg1216931811	A -> DEL	N	N	silent_mutation	Average:14.787; most accessible tissue: Callus, score: 42.051	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1216931811	4.14E-06	NA	mr1022_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