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Detailed information for vg0720872445:

Variant ID: vg0720872445 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 20872445
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTCGGGTTGTTTATTGATTGTTTCATATTTATGGCTTCTAGATGGATACTATACATATGTAATACTGTTGTTTGCTACTAATAAGTCAAGTTGGGGATA[G/A]
CTTGGTCTGGGAATATGGTTTCTTTGTTTGATTCATGTGTAGGTGACTTGATGCCTCGGGAGAGTATTTGCGGTGATGGATCGAGAGTCGACTTGGTGGT

Reverse complement sequence

ACCACCAAGTCGACTCTCGATCCATCACCGCAAATACTCTCCCGAGGCATCAAGTCACCTACACATGAATCAAACAAAGAAACCATATTCCCAGACCAAG[C/T]
TATCCCCAACTTGACTTATTAGTAGCAAACAACAGTATTACATATGTATAGTATCCATCTAGAAGCCATAAATATGAAACAATCAATAAACAACCCGAAA

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	21.90%	11.30%	2.20%	64.52%	NA
All Indica	2759	9.40%	10.90%	1.78%	77.89%	NA
All Japonica	1512	49.10%	1.70%	3.31%	45.83%	NA
Aus	269	0.70%	72.10%	0.74%	26.39%	NA
Indica I	595	11.30%	4.20%	1.34%	83.19%	NA
Indica II	465	9.20%	2.20%	1.72%	86.88%	NA
Indica III	913	1.30%	21.00%	2.08%	75.58%	NA
Indica Intermediate	786	17.40%	9.50%	1.78%	71.25%	NA
Temperate Japonica	767	49.00%	0.10%	5.22%	45.63%	NA
Tropical Japonica	504	42.90%	3.00%	1.19%	52.98%	NA
Japonica Intermediate	241	62.70%	4.10%	1.66%	31.54%	NA
VI/Aromatic	96	2.10%	5.20%	2.08%	90.62%	NA
Intermediate	90	34.40%	10.00%	1.11%	54.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0720872445	G -> DEL	N	N	silent_mutation	Average:11.052; most accessible tissue: Callus, score: 44.291	N	N	N	N
vg0720872445	G -> A	LOC_Os07g34830.1	upstream_gene_variant ; 1823.0bp to feature; MODIFIER	silent_mutation	Average:11.052; most accessible tissue: Callus, score: 44.291	N	N	N	N
vg0720872445	G -> A	LOC_Os07g34820.1	downstream_gene_variant ; 4599.0bp to feature; MODIFIER	silent_mutation	Average:11.052; most accessible tissue: Callus, score: 44.291	N	N	N	N
vg0720872445	G -> A	LOC_Os07g34820-LOC_Os07g34830	intergenic_region ; MODIFIER	silent_mutation	Average:11.052; most accessible tissue: Callus, score: 44.291	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0720872445	9.68E-08	NA	mr1261	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
vg0720872445	NA	2.81E-07	mr1261	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
vg0720872445	NA	1.50E-08	mr1707_2	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