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Detailed information for vg0710576171:

Variant ID: vg0710576171 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 10576171
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCCTTACCACCATGCGATGAGGCGTGGGAACGACAAAGACGAACGAGCGCGACGGAGACGGCTCAGGGACGACGGAGGCGAACGGCGAGGGAACGACTTC[G/A]
GCGGCGATCCTTGCACGAAGGCGAGACGCGGCCAGCACAAGGCTTGACGACACGGAGCCGAGGACGAAGACAACGACGGGGCTGCAGCGGCACACTTGAC

Reverse complement sequence

GTCAAGTGTGCCGCTGCAGCCCCGTCGTTGTCTTCGTCCTCGGCTCCGTGTCGTCAAGCCTTGTGCTGGCCGCGTCTCGCCTTCGTGCAAGGATCGCCGC[C/T]
GAAGTCGTTCCCTCGCCGTTCGCCTCCGTCGTCCCTGAGCCGTCTCCGTCGCGCTCGTTCGTCTTTGTCGTTCCCACGCCTCATCGCATGGTGGTAAGGA

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	95.10%	3.30%	1.67%	0.00%	NA
All Indica	2759	99.70%	0.10%	0.18%	0.00%	NA
All Japonica	1512	85.30%	9.90%	4.83%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	98.90%	0.60%	0.43%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.00%	0.25%	0.00%	NA
Temperate Japonica	767	74.20%	16.80%	9.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	91.30%	7.10%	1.66%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	1.10%	1.11%	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
vg0710576171	G -> A	LOC_Os07g17870.1	upstream_gene_variant ; 453.0bp to feature; MODIFIER	silent_mutation	Average:34.69; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg0710576171	G -> A	LOC_Os07g17880.1	upstream_gene_variant ; 4706.0bp to feature; MODIFIER	silent_mutation	Average:34.69; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg0710576171	G -> A	LOC_Os07g17860.1	downstream_gene_variant ; 2624.0bp to feature; MODIFIER	silent_mutation	Average:34.69; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg0710576171	G -> A	LOC_Os07g17860-LOC_Os07g17870	intergenic_region ; MODIFIER	silent_mutation	Average:34.69; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0710576171	NA	3.22E-06	mr1182	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
vg0710576171	3.50E-07	3.50E-07	mr1406	Jap_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