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Detailed information for vg1015419562:

Variant ID: vg1015419562 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 15419562
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATGTACTGTATAGTTGGCCCATGTCCAGCCCATCGGATGTCCAGCCCATTGGATCTTGTATCTTGTATATACTTCTCTATTGCTAATACTATTGTTAGGT[T/A]
GCAAGTTAGTTAAGACTCCTTTCTTTGCAGGATCCACCTGATTGGCATGAAATCCTTGCGTACTTCCATGGGTCTGAACTTCAGAATTACTTCAAGCGTA

Reverse complement sequence

TACGCTTGAAGTAATTCTGAAGTTCAGACCCATGGAAGTACGCAAGGATTTCATGCCAATCAGGTGGATCCTGCAAAGAAAGGAGTCTTAACTAACTTGC[A/T]
ACCTAACAATAGTATTAGCAATAGAGAAGTATATACAAGATACAAGATCCAATGGGCTGGACATCCGATGGGCTGGACATGGGCCAACTATACAGTACAT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	98.30%	1.00%	0.72%	0.00%	NA
All Indica	2759	97.70%	1.40%	0.87%	0.00%	NA
All Japonica	1512	99.90%	0.00%	0.07%	0.00%	NA
Aus	269	93.70%	3.00%	3.35%	0.00%	NA
Indica I	595	99.00%	0.50%	0.50%	0.00%	NA
Indica II	465	95.50%	2.80%	1.72%	0.00%	NA
Indica III	913	98.70%	1.00%	0.33%	0.00%	NA
Indica Intermediate	786	96.80%	1.90%	1.27%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	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
vg1015419562	T -> A	LOC_Os10g29650.3	5_prime_UTR_variant ; 1072.0bp to feature; MODIFIER	silent_mutation	Average:40.713; most accessible tissue: Minghui63 root, score: 62.438	N	N	N	N
vg1015419562	T -> A	LOC_Os10g29650.1	intron_variant ; MODIFIER	silent_mutation	Average:40.713; most accessible tissue: Minghui63 root, score: 62.438	N	N	N	N
vg1015419562	T -> A	LOC_Os10g29650.2	intron_variant ; MODIFIER	silent_mutation	Average:40.713; most accessible tissue: Minghui63 root, score: 62.438	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1015419562	1.81E-06	3.57E-06	mr1097	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