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Detailed information for vg1216280969:

Variant ID: vg1216280969 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 16280969
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTGACCTGCCCAAATAAATTACCTACTGGCCAAAATATGCCACAAACACTGGTTCTCCGCAGCAAGGCAACAATCTTCTCAGCGAAATGACCCCGATGGG[C/A]
AGCATTGTTTGGATTAACAAGCCGCTCGACCACAGTACAAACGCTGCGAGGCAGCCAGAGAAGGAGATGAGAGTTCATTGTTACCAGGCCCATATTTAGG

Reverse complement sequence

CCTAAATATGGGCCTGGTAACAATGAACTCTCATCTCCTTCTCTGGCTGCCTCGCAGCGTTTGTACTGTGGTCGAGCGGCTTGTTAATCCAAACAATGCT[G/T]
CCCATCGGGGTCATTTCGCTGAGAAGATTGTTGCCTTGCTGCGGAGAACCAGTGTTTGTGGCATATTTTGGCCAGTAGGTAATTTATTTGGGCAGGTCAG

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	86.80%	2.80%	0.15%	10.24%	NA
All Indica	2759	90.60%	4.60%	0.11%	4.64%	NA
All Japonica	1512	86.40%	0.10%	0.07%	13.43%	NA
Aus	269	45.00%	0.00%	1.12%	53.90%	NA
Indica I	595	87.90%	8.40%	0.00%	3.70%	NA
Indica II	465	89.00%	0.40%	0.22%	10.32%	NA
Indica III	913	93.40%	3.80%	0.00%	2.74%	NA
Indica Intermediate	786	90.50%	5.10%	0.25%	4.20%	NA
Temperate Japonica	767	99.70%	0.00%	0.00%	0.26%	NA
Tropical Japonica	504	62.50%	0.20%	0.20%	37.10%	NA
Japonica Intermediate	241	94.20%	0.00%	0.00%	5.81%	NA
VI/Aromatic	96	97.90%	1.00%	0.00%	1.04%	NA
Intermediate	90	90.00%	2.20%	0.00%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1216280969	C -> DEL	N	N	silent_mutation	Average:23.246; most accessible tissue: Callus, score: 67.536	N	N	N	N
vg1216280969	C -> A	LOC_Os12g27650.1	downstream_gene_variant ; 1088.0bp to feature; MODIFIER	silent_mutation	Average:23.246; most accessible tissue: Callus, score: 67.536	N	N	N	N
vg1216280969	C -> A	LOC_Os12g27650-LOC_Os12g27670	intergenic_region ; MODIFIER	silent_mutation	Average:23.246; most accessible tissue: Callus, score: 67.536	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1216280969	NA	8.04E-06	mr1008	Ind_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
vg1216280969	4.35E-06	NA	mr1103_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
vg1216280969	NA	2.36E-08	mr1458_2	Ind_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
vg1216280969	NA	8.73E-06	mr1971_2	Ind_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