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Detailed information for vg0523542913:

Variant ID: vg0523542913 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 23542913
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: 116. )

Flanking Sequence (100 bp) in Reference Genome:

GCCGATGATTGGTGGGTTTTCTAGAAAGTAAAAAATAAATTCTAACAATAGTTATGTTCGACTTTTACAGTCCCAATGATAATAAAGATTATGCGATGGA[C/T]
AGGTCGTAGAGAAGTATAGTGGCAACATTTGACGGAATTTCTAAAAATTATAAAAAACATGAAACCCAACGAGACAATAAAACTCACAATAAAACTCTAA

Reverse complement sequence

TTAGAGTTTTATTGTGAGTTTTATTGTCTCGTTGGGTTTCATGTTTTTTATAATTTTTAGAAATTCCGTCAAATGTTGCCACTATACTTCTCTACGACCT[G/A]
TCCATCGCATAATCTTTATTATCATTGGGACTGTAAAAGTCGAACATAACTATTGTTAGAATTTATTTTTTACTTTCTAGAAAACCCACCAATCATCGGC

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	64.40%	1.30%	26.36%	7.96%	NA
All Indica	2759	42.40%	2.10%	42.44%	13.12%	NA
All Japonica	1512	99.80%	0.00%	0.13%	0.07%	NA
Aus	269	77.30%	1.50%	18.59%	2.60%	NA
Indica I	595	27.90%	2.50%	44.54%	25.04%	NA
Indica II	465	33.50%	2.20%	43.87%	20.43%	NA
Indica III	913	53.50%	1.60%	40.42%	4.49%	NA
Indica Intermediate	786	45.70%	2.20%	42.37%	9.80%	NA
Temperate Japonica	767	99.60%	0.00%	0.26%	0.13%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	68.90%	0.00%	24.44%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0523542913	C -> T	LOC_Os05g40070.1	upstream_gene_variant ; 3900.0bp to feature; MODIFIER	silent_mutation	Average:18.101; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N
vg0523542913	C -> T	LOC_Os05g40070-LOC_Os05g40080	intergenic_region ; MODIFIER	silent_mutation	Average:18.101; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N
vg0523542913	C -> DEL	N	N	silent_mutation	Average:18.101; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0523542913	2.61E-06	NA	mr1039	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
vg0523542913	3.17E-06	NA	mr1039	Ind_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