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Detailed information for vg0719955551:

Variant ID: vg0719955551 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 19955551
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCCGGCGACCTCCCCCTCCCACCCCCTCTACCCCTACCCCAGTACCCCACATCTAGACCCTAATTCGTCGATCCTCTAGTAGAGTTTAGATTGACATCGG[C/T]
GACGAAGAAGAAGAATATATTGTCGGAGTTAGAGAATAAGCACATGTAGTAACAAATCGTGAAGAACATGCACTGATCCATAATCGGTAAAATTTGGGAA

Reverse complement sequence

TTCCCAAATTTTACCGATTATGGATCAGTGCATGTTCTTCACGATTTGTTACTACATGTGCTTATTCTCTAACTCCGACAATATATTCTTCTTCTTCGTC[G/A]
CCGATGTCAATCTAAACTCTACTAGAGGATCGACGAATTAGGGTCTAGATGTGGGGTACTGGGGTAGGGGTAGAGGGGGTGGGAGGGGGAGGTCGCCGGG

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	92.80%	7.20%	0.02%	0.00%	NA
All Indica	2759	97.40%	2.60%	0.04%	0.00%	NA
All Japonica	1512	88.70%	11.30%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	89.00%	10.80%	0.22%	0.00%	NA
Indica III	913	99.00%	1.00%	0.00%	0.00%	NA
Indica Intermediate	786	98.50%	1.50%	0.00%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	68.30%	31.70%	0.00%	0.00%	NA
Japonica Intermediate	241	96.30%	3.70%	0.00%	0.00%	NA
VI/Aromatic	96	11.50%	88.50%	0.00%	0.00%	NA
Intermediate	90	85.60%	14.40%	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
vg0719955551	C -> T	LOC_Os07g33370.1	upstream_gene_variant ; 4496.0bp to feature; MODIFIER	silent_mutation	Average:57.92; most accessible tissue: Zhenshan97 young leaf, score: 73.54	N	N	N	N
vg0719955551	C -> T	LOC_Os07g33380.1	upstream_gene_variant ; 1682.0bp to feature; MODIFIER	silent_mutation	Average:57.92; most accessible tissue: Zhenshan97 young leaf, score: 73.54	N	N	N	N
vg0719955551	C -> T	LOC_Os07g33370-LOC_Os07g33380	intergenic_region ; MODIFIER	silent_mutation	Average:57.92; most accessible tissue: Zhenshan97 young leaf, score: 73.54	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0719955551	4.80E-06	NA	mr1584	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
vg0719955551	NA	7.23E-07	mr1584	Jap_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