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Detailed information for vg0415966817:

Variant ID: vg0415966817 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 15966817
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CACTTGGTTGACTATAATTATCGAAAACCACTCAGTTGGTTGGATTATTTACTCCTTAAATATATGTTCAGTTTGTTCAACTAACCACATAGTCGGGGGC[T/A]
ACACCTATTAGGTGCATCTAATCGATGCACCTAAGATTACATTTAATTATTTCTCAGCCCTCCACAGTCTTCAGATTTGGTAAAAGTACTTGGGAGATCT

Reverse complement sequence

AGATCTCCCAAGTACTTTTACCAAATCTGAAGACTGTGGAGGGCTGAGAAATAATTAAATGTAATCTTAGGTGCATCGATTAGATGCACCTAATAGGTGT[A/T]
GCCCCCGACTATGTGGTTAGTTGAACAAACTGAACATATATTTAAGGAGTAAATAATCCAACCAACTGAGTGGTTTTCGATAATTATAGTCAACCAAGTG

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	96.60%	1.10%	2.07%	0.23%	NA
All Indica	2759	95.90%	1.30%	2.39%	0.40%	NA
All Japonica	1512	99.80%	0.00%	0.20%	0.00%	NA
Aus	269	96.70%	1.90%	1.49%	0.00%	NA
Indica I	595	99.50%	0.20%	0.34%	0.00%	NA
Indica II	465	94.40%	2.80%	1.29%	1.51%	NA
Indica III	913	98.00%	0.50%	1.20%	0.22%	NA
Indica Intermediate	786	91.60%	2.20%	5.98%	0.25%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	99.20%	0.00%	0.83%	0.00%	NA
VI/Aromatic	96	67.70%	10.40%	21.88%	0.00%	NA
Intermediate	90	94.40%	1.10%	4.44%	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
vg0415966817	T -> DEL	N	N	silent_mutation	Average:28.09; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg0415966817	T -> A	LOC_Os04g26994.1	upstream_gene_variant ; 2013.0bp to feature; MODIFIER	silent_mutation	Average:28.09; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg0415966817	T -> A	LOC_Os04g26980-LOC_Os04g26994	intergenic_region ; MODIFIER	silent_mutation	Average:28.09; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0415966817	NA	3.62E-10	mr1927	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