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Detailed information for vg1015871199:

Variant ID: vg1015871199 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 15871199
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTATTCCTTGTTGGGTGTAGTGTTGTAATATTTCACATTAATTCTTCCAGCTTTCCAGCTTATTTTATTCTCTGTTCAGTTACTCTATGTTCCTTCAGAA[C/T]
TCAAATCAGTTTGGCACTTTCTGGGGAGCAAACACATTTATGTATCACATATTGATGCATCCATTGTTTTTTTTTCTACAGCTAATAATGCTGGAGGGGT

Reverse complement sequence

ACCCCTCCAGCATTATTAGCTGTAGAAAAAAAAACAATGGATGCATCAATATGTGATACATAAATGTGTTTGCTCCCCAGAAAGTGCCAAACTGATTTGA[G/A]
TTCTGAAGGAACATAGAGTAACTGAACAGAGAATAAAATAAGCTGGAAAGCTGGAAGAATTAATGTGAAATATTACAACACTACACCCAACAAGGAATAG

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	89.10%	10.90%	0.02%	0.00%	NA
All Indica	2759	99.40%	0.60%	0.00%	0.00%	NA
All Japonica	1512	69.90%	30.00%	0.07%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	98.50%	1.50%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	98.70%	1.30%	0.00%	0.00%	NA
Temperate Japonica	767	97.50%	2.50%	0.00%	0.00%	NA
Tropical Japonica	504	22.40%	77.40%	0.20%	0.00%	NA
Japonica Intermediate	241	81.30%	18.70%	0.00%	0.00%	NA
VI/Aromatic	96	72.90%	27.10%	0.00%	0.00%	NA
Intermediate	90	83.30%	16.70%	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
vg1015871199	C -> T	LOC_Os10g30530.1	upstream_gene_variant ; 2948.0bp to feature; MODIFIER	silent_mutation	Average:47.719; most accessible tissue: Callus, score: 83.083	N	N	N	N
vg1015871199	C -> T	LOC_Os10g30510.1	downstream_gene_variant ; 2867.0bp to feature; MODIFIER	silent_mutation	Average:47.719; most accessible tissue: Callus, score: 83.083	N	N	N	N
vg1015871199	C -> T	LOC_Os10g30520.1	intron_variant ; MODIFIER	silent_mutation	Average:47.719; most accessible tissue: Callus, score: 83.083	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1015871199	4.56E-07	4.56E-07	mr1848	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