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Detailed information for vg1222786386:

Variant ID: vg1222786386 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 22786386
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGACTAAACATTAGCTCTCAAAATTAACCCTGGGCTAATCTTCCAAATAGAGCCTAGCTAGCCTGAAATTTGTGCTGCCTGTGGAAATGCGGGTCAGTGC[C/T]
GGAGTTGCACGGCCGCTGGATGGGCTAATGTTTAGCCTATCAATTCATGACTAAATATTAGCTCTCAAAATTAGCTCTGGACTAATCTTCCAAATAGAGC

Reverse complement sequence

GCTCTATTTGGAAGATTAGTCCAGAGCTAATTTTGAGAGCTAATATTTAGTCATGAATTGATAGGCTAAACATTAGCCCATCCAGCGGCCGTGCAACTCC[G/A]
GCACTGACCCGCATTTCCACAGGCAGCACAAATTTCAGGCTAGCTAGGCTCTATTTGGAAGATTAGCCCAGGGTTAATTTTGAGAGCTAATGTTTAGTCA

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	53.60%	3.60%	6.09%	36.78%	NA
All Indica	2759	33.10%	1.00%	3.81%	62.16%	NA
All Japonica	1512	84.30%	4.10%	11.04%	0.60%	NA
Aus	269	65.10%	29.00%	4.09%	1.86%	NA
Indica I	595	62.00%	0.20%	6.55%	31.26%	NA
Indica II	465	26.70%	0.20%	7.74%	65.38%	NA
Indica III	913	19.10%	1.90%	0.88%	78.20%	NA
Indica Intermediate	786	31.20%	1.00%	2.80%	65.01%	NA
Temperate Japonica	767	74.80%	7.40%	17.34%	0.39%	NA
Tropical Japonica	504	96.40%	0.00%	2.58%	0.99%	NA
Japonica Intermediate	241	88.80%	2.10%	8.71%	0.41%	NA
VI/Aromatic	96	96.90%	1.00%	0.00%	2.08%	NA
Intermediate	90	85.60%	1.10%	5.56%	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
vg1222786386	C -> DEL	N	N	silent_mutation	Average:25.882; most accessible tissue: Zhenshan97 panicle, score: 43.098	N	N	N	N
vg1222786386	C -> T	LOC_Os12g37160.1	upstream_gene_variant ; 617.0bp to feature; MODIFIER	silent_mutation	Average:25.882; most accessible tissue: Zhenshan97 panicle, score: 43.098	N	N	N	N
vg1222786386	C -> T	LOC_Os12g37160.3	upstream_gene_variant ; 617.0bp to feature; MODIFIER	silent_mutation	Average:25.882; most accessible tissue: Zhenshan97 panicle, score: 43.098	N	N	N	N
vg1222786386	C -> T	LOC_Os12g37160.2	upstream_gene_variant ; 611.0bp to feature; MODIFIER	silent_mutation	Average:25.882; most accessible tissue: Zhenshan97 panicle, score: 43.098	N	N	N	N
vg1222786386	C -> T	LOC_Os12g37160-LOC_Os12g37180	intergenic_region ; MODIFIER	silent_mutation	Average:25.882; most accessible tissue: Zhenshan97 panicle, score: 43.098	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1222786386	3.59E-06	NA	mr1245	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