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Detailed information for vg0921125028:

Variant ID: vg0921125028 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 21125028
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GACTCCTAGTATGAGTTTGGTTCGTGGCTTTAGGCTGCCTACCTCATGTATAAATAGAGGGGGAGCGTGAGGCTTCCCTGTATCGCTTTAGAGAGTAATA[G/T]
AGTTGAGTTTTGAGTTAGGGTTTCGAGTTTAGTCGAAATTTTTGTAAGGAGTGCTGTTGGTGCACTTTGTAAATACAGAGAGAATCAATAAAGTCGTCAT

Reverse complement sequence

ATGACGACTTTATTGATTCTCTCTGTATTTACAAAGTGCACCAACAGCACTCCTTACAAAAATTTCGACTAAACTCGAAACCCTAACTCAAAACTCAACT[C/A]
TATTACTCTCTAAAGCGATACAGGGAAGCCTCACGCTCCCCCTCTATTTATACATGAGGTAGGCAGCCTAAAGCCACGAACCAAACTCATACTAGGAGTC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	75.00%	6.10%	18.96%	0.00%	NA
All Indica	2759	57.60%	10.20%	32.19%	0.00%	NA
All Japonica	1512	99.90%	0.00%	0.07%	0.00%	NA
Aus	269	98.90%	0.70%	0.37%	0.00%	NA
Indica I	595	24.70%	13.30%	62.02%	0.00%	NA
Indica II	465	77.20%	4.50%	18.28%	0.00%	NA
Indica III	913	64.50%	13.70%	21.80%	0.00%	NA
Indica Intermediate	786	62.80%	7.30%	29.90%	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	91.10%	2.20%	6.67%	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
vg0921125028	G -> T	LOC_Os09g36610.1	downstream_gene_variant ; 1985.0bp to feature; MODIFIER	silent_mutation	Average:30.661; most accessible tissue: Minghui63 root, score: 57.225	N	N	N	N
vg0921125028	G -> T	LOC_Os09g36610-LOC_Os09g36619	intergenic_region ; MODIFIER	silent_mutation	Average:30.661; most accessible tissue: Minghui63 root, score: 57.225	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0921125028	2.15E-06	NA	mr1295	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
vg0921125028	4.23E-06	1.61E-06	mr1295	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