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Detailed information for vg1010397045:

Variant ID: vg1010397045 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 10397045
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:

CTATCGTGAGACAGGAAGACATGCATGTGAGAAGAATTAAGCGCGGGCGCTACCATGCAAATTAATCACGCCAAAACGCATTAGACCATCTCCACGATTA[G/A]
TTGGCTAGCTGGTTTCCTCTTGCATACCGTTCCTTGCATGCATGTGTAGATGATGGAAAAATATGTAGCGTAAACTTCATATATATAATGTACTATCTTC

Reverse complement sequence

GAAGATAGTACATTATATATATGAAGTTTACGCTACATATTTTTCCATCATCTACACATGCATGCAAGGAACGGTATGCAAGAGGAAACCAGCTAGCCAA[C/T]
TAATCGTGGAGATGGTCTAATGCGTTTTGGCGTGATTAATTTGCATGGTAGCGCCCGCGCTTAATTCTTCTCACATGCATGTCTTCCTGTCTCACGATAG

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	94.20%	4.50%	1.21%	0.00%	NA
All Indica	2759	90.50%	7.60%	1.81%	0.00%	NA
All Japonica	1512	99.70%	0.10%	0.20%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	92.30%	4.40%	3.36%	0.00%	NA
Indica II	465	85.20%	12.00%	2.80%	0.00%	NA
Indica III	913	95.20%	4.50%	0.33%	0.00%	NA
Indica Intermediate	786	87.00%	11.20%	1.78%	0.00%	NA
Temperate Japonica	767	99.70%	0.00%	0.26%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	92.20%	3.30%	4.44%	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
vg1010397045	G -> A	LOC_Os10g20610.1	upstream_gene_variant ; 425.0bp to feature; MODIFIER	silent_mutation	Average:53.95; most accessible tissue: Zhenshan97 root, score: 90.472	N	N	N	N
vg1010397045	G -> A	LOC_Os10g20610-LOC_Os10g20630	intergenic_region ; MODIFIER	silent_mutation	Average:53.95; most accessible tissue: Zhenshan97 root, score: 90.472	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1010397045	2.41E-06	NA	mr1161_2	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