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Detailed information for vg0522746391:

Variant ID: vg0522746391 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 22746391
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTCGTGCAGGTACTCCAGCCCCTGCGCTGCGCCGTACGCCACCTTCATCCTCGTGCACCAGTCCATCGGCTTCTTGTCCGCCGGCAAATCTGCCGACGAC[G/A]
ACGATGCAACAATAACAGAACAATGGACAATCTCATTATCGTCGTCTTAGAGTATTCGTTCGCGTTGCGGCGTGTGGTGGGTGTGCGTACCGAACAAGTG

Reverse complement sequence

CACTTGTTCGGTACGCACACCCACCACACGCCGCAACGCGAACGAATACTCTAAGACGACGATAATGAGATTGTCCATTGTTCTGTTATTGTTGCATCGT[C/T]
GTCGTCGGCAGATTTGCCGGCGGACAAGAAGCCGATGGACTGGTGCACGAGGATGAAGGTGGCGTACGGCGCAGCGCAGGGGCTGGAGTACCTGCACGAG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	96.20%	3.80%	0.00%	0.00%	NA
All Indica	2759	93.50%	6.50%	0.00%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	97.80%	2.20%	0.00%	0.00%	NA
Indica II	465	92.90%	7.10%	0.00%	0.00%	NA
Indica III	913	89.00%	11.00%	0.00%	0.00%	NA
Indica Intermediate	786	95.90%	4.10%	0.00%	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	100.00%	0.00%	0.00%	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
vg0522746391	G -> A	LOC_Os05g38760.1	upstream_gene_variant ; 1939.0bp to feature; MODIFIER	silent_mutation	Average:63.742; most accessible tissue: Minghui63 young leaf, score: 80.883	N	N	N	N
vg0522746391	G -> A	LOC_Os05g38770.1	intron_variant ; MODIFIER	silent_mutation	Average:63.742; most accessible tissue: Minghui63 young leaf, score: 80.883	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0522746391	NA	7.77E-06	mr1671	Ind_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