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Detailed information for vg0716931835:

Variant ID: vg0716931835 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 16931835
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCTTTTACTTACTTTATTATCTAAAATACTTTAAACATAACTTTTTATTTTTTATATTTGCATAAATTTTTTGAATAAAATGAGTGGTCAAATATTGTAA[G/A]
AAAAACTTAAAATCCCTTATATTATGGGACGGAGGGAGTCCAGTACACTACCACTGCATTCACTCTCACACAGTACATATATACTTCCTCACTAAGCATA

Reverse complement sequence

TATGCTTAGTGAGGAAGTATATATGTACTGTGTGAGAGTGAATGCAGTGGTAGTGTACTGGACTCCCTCCGTCCCATAATATAAGGGATTTTAAGTTTTT[C/T]
TTACAATATTTGACCACTCATTTTATTCAAAAAATTTATGCAAATATAAAAAATAAAAAGTTATGTTTAAAGTATTTTAGATAATAAAGTAAGTAAAAGA

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	84.70%	10.80%	3.89%	0.59%	NA
All Indica	2759	98.10%	0.20%	1.01%	0.69%	NA
All Japonica	1512	57.10%	32.30%	9.92%	0.60%	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	98.90%	0.20%	0.65%	0.22%	NA
Indica III	913	98.60%	0.30%	0.99%	0.11%	NA
Indica Intermediate	786	95.70%	0.10%	2.04%	2.16%	NA
Temperate Japonica	767	71.60%	17.60%	9.65%	1.17%	NA
Tropical Japonica	504	44.00%	48.80%	7.14%	0.00%	NA
Japonica Intermediate	241	38.60%	44.80%	16.60%	0.00%	NA
VI/Aromatic	96	95.80%	3.10%	1.04%	0.00%	NA
Intermediate	90	77.80%	16.70%	5.56%	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
vg0716931835	G -> DEL	N	N	silent_mutation	Average:74.846; most accessible tissue: Minghui63 root, score: 86.528	N	N	N	N
vg0716931835	G -> A	LOC_Os07g28890.1	upstream_gene_variant ; 1928.0bp to feature; MODIFIER	silent_mutation	Average:74.846; most accessible tissue: Minghui63 root, score: 86.528	N	N	N	N
vg0716931835	G -> A	LOC_Os07g28880.1	downstream_gene_variant ; 346.0bp to feature; MODIFIER	silent_mutation	Average:74.846; most accessible tissue: Minghui63 root, score: 86.528	N	N	N	N
vg0716931835	G -> A	LOC_Os07g28870-LOC_Os07g28880	intergenic_region ; MODIFIER	silent_mutation	Average:74.846; most accessible tissue: Minghui63 root, score: 86.528	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0716931835	3.98E-07	NA	mr1238	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
vg0716931835	3.23E-07	NA	mr1309	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
vg0716931835	NA	1.92E-08	mr1354	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
vg0716931835	NA	6.83E-06	mr1398	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
vg0716931835	1.04E-06	1.90E-12	mr1554	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
vg0716931835	NA	2.23E-13	mr1578	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
vg0716931835	3.77E-06	2.60E-09	mr1602	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
vg0716931835	NA	3.62E-12	mr1819	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
vg0716931835	1.30E-06	8.06E-18	mr1900	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
vg0716931835	NA	1.83E-06	mr1900	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
vg0716931835	2.25E-06	4.41E-10	mr1945	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
vg0716931835	NA	2.27E-07	mr1369_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
vg0716931835	NA	9.57E-08	mr1453_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
vg0716931835	NA	1.58E-07	mr1554_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
vg0716931835	NA	5.38E-10	mr1851_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
vg0716931835	NA	2.26E-06	mr1966_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