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Detailed information for vg0207526789:

Variant ID: vg0207526789 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 7526789
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AACATTACAAGTACACTAAGTGAAACATTTTTCGGTGGAACAAAAAATAAAATGAATTCCCTTAATAGGAGGTTTCCAAAATATGTGGTTTTTTTTGTTG[C/T]
AATGGAATATTTCAGTTCACTGCAATATTAGATCTATATATAGTGAAACATTGTGAGTACACTAGGTGAAACATTTTTTATGGAAAAAAAAATAAACCGA

Reverse complement sequence

TCGGTTTATTTTTTTTTCCATAAAAAATGTTTCACCTAGTGTACTCACAATGTTTCACTATATATAGATCTAATATTGCAGTGAACTGAAATATTCCATT[G/A]
CAACAAAAAAAACCACATATTTTGGAAACCTCCTATTAAGGGAATTCATTTTATTTTTTGTTCCACCGAAAAATGTTTCACTTAGTGTACTTGTAATGTT

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	92.00%	7.40%	0.44%	0.15%	NA
All Indica	2759	98.20%	1.20%	0.33%	0.25%	NA
All Japonica	1512	80.10%	19.20%	0.66%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	98.90%	0.40%	0.22%	0.43%	NA
Indica III	913	96.60%	2.40%	0.55%	0.44%	NA
Indica Intermediate	786	98.50%	1.00%	0.38%	0.13%	NA
Temperate Japonica	767	83.60%	15.50%	0.91%	0.00%	NA
Tropical Japonica	504	69.20%	30.20%	0.60%	0.00%	NA
Japonica Intermediate	241	91.70%	8.30%	0.00%	0.00%	NA
VI/Aromatic	96	81.20%	16.70%	2.08%	0.00%	NA
Intermediate	90	91.10%	8.90%	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
vg0207526789	C -> T	LOC_Os02g13880.1	upstream_gene_variant ; 2226.0bp to feature; MODIFIER	silent_mutation	Average:37.771; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg0207526789	C -> T	LOC_Os02g13880-LOC_Os02g13890	intergenic_region ; MODIFIER	silent_mutation	Average:37.771; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg0207526789	C -> DEL	N	N	silent_mutation	Average:37.771; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0207526789	4.08E-06	1.98E-07	mr1783	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