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Detailed information for vg0800007834:

Variant ID: vg0800007834 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 7834
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTGCGAGAGATTGCTACGTACTGGTTCGAGAACCAGCGAGCGAGTAGAATTATCTCGAGAACACCAATGGGAGTTGCGGTGCGAGAGATTGCTACGTACT[G/A]
GTTTGAGAACCAGCGAGCGAGTAGAATTATCTCTCAAACACCAATGGAGGCGCTAGAGTTGGTTTATTACATGTGCATCTCATGTGGCCAGCATGACTCA

Reverse complement sequence

TGAGTCATGCTGGCCACATGAGATGCACATGTAATAAACCAACTCTAGCGCCTCCATTGGTGTTTGAGAGATAATTCTACTCGCTCGCTGGTTCTCAAAC[C/T]
AGTACGTAGCAATCTCTCGCACCGCAACTCCCATTGGTGTTCTCGAGATAATTCTACTCGCTCGCTGGTTCTCGAACCAGTACGTAGCAATCTCTCGCAC

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	81.00%	1.20%	4.04%	13.73%	NA
All Indica	2759	78.00%	1.40%	4.17%	16.46%	NA
All Japonica	1512	89.20%	0.10%	0.40%	10.32%	NA
Aus	269	62.50%	5.90%	23.05%	8.55%	NA
Indica I	595	92.10%	0.00%	0.00%	7.90%	NA
Indica II	465	45.60%	0.20%	3.44%	50.75%	NA
Indica III	913	90.30%	1.80%	5.37%	2.63%	NA
Indica Intermediate	786	72.10%	2.80%	6.36%	18.70%	NA
Temperate Japonica	767	98.00%	0.00%	0.00%	1.96%	NA
Tropical Japonica	504	75.40%	0.20%	1.19%	23.21%	NA
Japonica Intermediate	241	90.00%	0.00%	0.00%	9.96%	NA
VI/Aromatic	96	97.90%	0.00%	1.04%	1.04%	NA
Intermediate	90	74.40%	1.10%	7.78%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0800007834	G -> A	LOC_Os08g01010.1	splice_region_variant&intron_variant ; LOW	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0800007834	G -> A	LOC_Os08g01020.1	upstream_gene_variant ; 2352.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0800007834	G -> A	LOC_Os08g01008.1	downstream_gene_variant ; 2898.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0800007834	G -> DEL	N	N	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0800007834	NA	1.66E-06	mr1291	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
vg0800007834	2.89E-06	3.91E-13	mr1471	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
vg0800007834	NA	2.98E-07	mr1577	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
vg0800007834	NA	8.14E-06	mr1654	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
vg0800007834	NA	1.22E-06	mr1684	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
vg0800007834	NA	2.44E-07	mr1808	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
vg0800007834	NA	1.52E-08	mr1815	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
vg0800007834	NA	7.07E-08	mr1808_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