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Detailed information for vg1004358089:

Variant ID: vg1004358089 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 4358089
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAACTAACCATCTCGTGGGCAAAATGGAAGGTTTCCAGGACAAACCTACGAAGAGGTGTCGCACTCTCGCAGCGGCGGCGGACGGTTTACAGCGCAAACC[G/A]
ACAAAGATGAACTAAAACTAGGGTAAAATAGAAAACATAGTAAAAGAATGATTCAAGTATATTGTATTTGGAGGTTTTACAATGAACAGGCCTTGTCCCT

Reverse complement sequence

AGGGACAAGGCCTGTTCATTGTAAAACCTCCAAATACAATATACTTGAATCATTCTTTTACTATGTTTTCTATTTTACCCTAGTTTTAGTTCATCTTTGT[C/T]
GGTTTGCGCTGTAAACCGTCCGCCGCCGCTGCGAGAGTGCGACACCTCTTCGTAGGTTTGTCCTGGAAACCTTCCATTTTGCCCACGAGATGGTTAGTTA

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	43.70%	0.10%	8.34%	47.82%	NA
All Indica	2759	28.10%	0.10%	7.54%	64.19%	NA
All Japonica	1512	60.10%	0.10%	10.91%	28.84%	NA
Aus	269	97.40%	0.00%	0.00%	2.60%	NA
Indica I	595	43.90%	0.00%	3.53%	52.61%	NA
Indica II	465	25.80%	0.20%	4.52%	69.46%	NA
Indica III	913	21.90%	0.10%	10.62%	67.36%	NA
Indica Intermediate	786	24.80%	0.30%	8.78%	66.16%	NA
Temperate Japonica	767	85.80%	0.00%	0.39%	13.82%	NA
Tropical Japonica	504	19.00%	0.20%	29.76%	50.99%	NA
Japonica Intermediate	241	64.30%	0.40%	4.98%	30.29%	NA
VI/Aromatic	96	72.90%	0.00%	12.50%	14.58%	NA
Intermediate	90	54.40%	0.00%	10.00%	35.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1004358089	G -> A	LOC_Os10g08030.1	upstream_gene_variant ; 2500.0bp to feature; MODIFIER	silent_mutation	Average:39.621; most accessible tissue: Zhenshan97 panicle, score: 57.341	N	N	N	N
vg1004358089	G -> A	LOC_Os10g08040.1	intron_variant ; MODIFIER	silent_mutation	Average:39.621; most accessible tissue: Zhenshan97 panicle, score: 57.341	N	N	N	N
vg1004358089	G -> DEL	N	N	silent_mutation	Average:39.621; most accessible tissue: Zhenshan97 panicle, score: 57.341	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1004358089	2.82E-06	1.02E-07	mr1633	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