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Detailed information for vg1216034113:

Variant ID: vg1216034113 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 16034113
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATGCACAAATCTCCATCGTTTCTACTCTAGTTGATTAGCACATGTATGTAAAAAGTCTATAGGCTTGCGCATGCATGACTGCATGGTTCAGCACTTATCT[C/T]
AACCCTATTTTTTATTTCTTCTAAATTAATTATCTAATTTATGATTCGATTTCACCATTAAACTCCTTGCAATTGAATCTTCATAACAAGATCTTGCACG

Reverse complement sequence

CGTGCAAGATCTTGTTATGAAGATTCAATTGCAAGGAGTTTAATGGTGAAATCGAATCATAAATTAGATAATTAATTTAGAAGAAATAAAAAATAGGGTT[G/A]
AGATAAGTGCTGAACCATGCAGTCATGCATGCGCAAGCCTATAGACTTTTTACATACATGTGCTAATCAACTAGAGTAGAAACGATGGAGATTTGTGCAT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	50.10%	18.50%	17.94%	13.54%	NA
All Indica	2759	43.20%	29.70%	25.70%	1.45%	NA
All Japonica	1512	64.90%	0.50%	0.93%	33.60%	NA
Aus	269	20.80%	13.40%	39.03%	26.77%	NA
Indica I	595	48.90%	18.00%	32.61%	0.50%	NA
Indica II	465	30.80%	35.50%	32.04%	1.72%	NA
Indica III	913	44.10%	40.10%	15.12%	0.66%	NA
Indica Intermediate	786	45.00%	23.00%	29.01%	2.93%	NA
Temperate Japonica	767	95.60%	0.40%	0.52%	3.52%	NA
Tropical Japonica	504	13.70%	0.40%	1.39%	84.52%	NA
Japonica Intermediate	241	74.70%	1.20%	1.24%	22.82%	NA
VI/Aromatic	96	83.30%	2.10%	5.21%	9.38%	NA
Intermediate	90	63.30%	7.80%	16.67%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1216034113	C -> DEL	N	N	silent_mutation	Average:32.639; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg1216034113	C -> T	LOC_Os12g27280.1	upstream_gene_variant ; 4446.0bp to feature; MODIFIER	silent_mutation	Average:32.639; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg1216034113	C -> T	LOC_Os12g27290.1	downstream_gene_variant ; 63.0bp to feature; MODIFIER	silent_mutation	Average:32.639; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg1216034113	C -> T	LOC_Os12g27290-LOC_Os12g27300	intergenic_region ; MODIFIER	silent_mutation	Average:32.639; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1216034113	NA	6.24E-07	mr1709	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
vg1216034113	1.93E-07	3.00E-07	mr1739	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
vg1216034113	6.62E-06	1.24E-09	mr1739	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