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Detailed information for vg0612661215:

Variant ID: vg0612661215 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 12661215
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 327. )

Flanking Sequence (100 bp) in Reference Genome:

AAAACCTAGCTAGGTCCTACATTGTTTTCTCCGTCTCATCATTGGCGTAGCATTCATAAGGTCATCTCCGAGACATCCTTCTAAAAGAGTTAATTAAGCA[C/T]
GTGTGAGTACCAACTGTACTTAGCAAGCTAGTACTACATAATACATTAGTGCACACAGGGTTCAACCCTTCAAGGATGGCTAGGTTTATTCGCATAAAAT

Reverse complement sequence

ATTTTATGCGAATAAACCTAGCCATCCTTGAAGGGTTGAACCCTGTGTGCACTAATGTATTATGTAGTACTAGCTTGCTAAGTACAGTTGGTACTCACAC[G/A]
TGCTTAATTAACTCTTTTAGAAGGATGTCTCGGAGATGACCTTATGAATGCTACGCCAATGATGAGACGGAGAAAACAATGTAGGACCTAGCTAGGTTTT

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	97.70%	2.10%	0.19%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.04%	0.00%	NA
All Japonica	1512	93.30%	6.30%	0.46%	0.00%	NA
Aus	269	98.90%	0.70%	0.37%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	92.70%	6.40%	0.91%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	81.30%	18.70%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0612661215	C -> T	LOC_Os06g21900.1	downstream_gene_variant ; 2121.0bp to feature; MODIFIER	silent_mutation	Average:42.276; most accessible tissue: Callus, score: 70.117	N	N	N	N
vg0612661215	C -> T	LOC_Os06g21910.1	downstream_gene_variant ; 4371.0bp to feature; MODIFIER	silent_mutation	Average:42.276; most accessible tissue: Callus, score: 70.117	N	N	N	N
vg0612661215	C -> T	LOC_Os06g21900-LOC_Os06g21910	intergenic_region ; MODIFIER	silent_mutation	Average:42.276; most accessible tissue: Callus, score: 70.117	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0612661215	2.64E-06	2.64E-06	mr1141	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