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Detailed information for vg1216138559:

Variant ID: vg1216138559 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 16138559
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGATTGGTGCTCCCTGATTTTTACTGCTTTCCTTCTCTTGTTACAAACTCTTTTGTGGGTTTGTGTGTTTTGGCTGTGTGCATCCTAGTTATGCAGAGGC[C/T]
GGGAGTTTTCTTAGTATGGTTCTATCAACTTGATGTAATCGTCTGAGATTAATAAAAGCTTCCTTTATAAAAAAAAATTAAAACAACGCAACAAGATATA

Reverse complement sequence

TATATCTTGTTGCGTTGTTTTAATTTTTTTTTATAAAGGAAGCTTTTATTAATCTCAGACGATTACATCAAGTTGATAGAACCATACTAAGAAAACTCCC[G/A]
GCCTCTGCATAACTAGGATGCACACAGCCAAAACACACAAACCCACAAAAGAGTTTGTAACAAGAGAAGGAAAGCAGTAAAAATCAGGGAGCACCAATCC

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	28.00%	1.40%	20.25%	50.38%	NA
All Indica	2759	7.90%	0.00%	30.37%	61.73%	NA
All Japonica	1512	60.80%	4.10%	3.90%	31.15%	NA
Aus	269	24.20%	0.00%	14.50%	61.34%	NA
Indica I	595	11.30%	0.00%	28.24%	60.50%	NA
Indica II	465	9.70%	0.00%	32.26%	58.06%	NA
Indica III	913	2.50%	0.00%	32.64%	64.84%	NA
Indica Intermediate	786	10.40%	0.10%	28.24%	61.20%	NA
Temperate Japonica	767	89.40%	5.70%	0.39%	4.43%	NA
Tropical Japonica	504	13.90%	0.20%	9.92%	75.99%	NA
Japonica Intermediate	241	68.00%	7.10%	2.49%	22.41%	NA
VI/Aromatic	96	82.30%	0.00%	2.08%	15.62%	NA
Intermediate	90	47.80%	1.10%	21.11%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1216138559	C -> DEL	N	N	silent_mutation	Average:21.433; most accessible tissue: Callus, score: 55.096	N	N	N	N
vg1216138559	C -> T	LOC_Os12g27410.1	downstream_gene_variant ; 106.0bp to feature; MODIFIER	silent_mutation	Average:21.433; most accessible tissue: Callus, score: 55.096	N	N	N	N
vg1216138559	C -> T	LOC_Os12g27420.1	downstream_gene_variant ; 1280.0bp to feature; MODIFIER	silent_mutation	Average:21.433; most accessible tissue: Callus, score: 55.096	N	N	N	N
vg1216138559	C -> T	LOC_Os12g27430.1	downstream_gene_variant ; 3845.0bp to feature; MODIFIER	silent_mutation	Average:21.433; most accessible tissue: Callus, score: 55.096	N	N	N	N
vg1216138559	C -> T	LOC_Os12g27410-LOC_Os12g27420	intergenic_region ; MODIFIER	silent_mutation	Average:21.433; most accessible tissue: Callus, score: 55.096	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1216138559	2.09E-06	2.09E-06	mr1651	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
vg1216138559	7.95E-06	7.95E-06	mr1750	Jap_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