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Detailed information for vg1000213979:

Variant ID: vg1000213979 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 213979
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.51, G: 0.49, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

CGAGTACACTTGATGCTGCCGAAATCTTCGACAAACTGAGAGTCGCTCCGGATACTTACTTCAAGAACATCAAAGAAGCTGGAAGTATGAGAGCAAGTCT[A/G]
GCGCTGGCGATGACCAAATCCCTTTATCCAAGAGTTGACATGGATGCCATTGATGGCTTTGCAGACGGGACGGGCAAAGAAGCTGCTCTTGACCTCATCA

Reverse complement sequence

TGATGAGGTCAAGAGCAGCTTCTTTGCCCGTCCCGTCTGCAAAGCCATCAATGGCATCCATGTCAACTCTTGGATAAAGGGATTTGGTCATCGCCAGCGC[T/C]
AGACTTGCTCTCATACTTCCAGCTTCTTTGATGTTCTTGAAGTAAGTATCCGGAGCGACTCTCAGTTTGTCGAAGATTTCGGCAGCATCAAGTGTACTCG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	19.10%	17.90%	0.93%	62.12%	NA
All Indica	2759	1.40%	28.70%	1.23%	68.68%	NA
All Japonica	1512	54.50%	1.50%	0.40%	43.58%	NA
Aus	269	3.30%	5.60%	0.00%	91.08%	NA
Indica I	595	2.40%	18.70%	1.85%	77.14%	NA
Indica II	465	1.30%	46.20%	0.65%	51.83%	NA
Indica III	913	0.50%	23.30%	0.77%	75.36%	NA
Indica Intermediate	786	1.80%	32.10%	1.65%	64.50%	NA
Temperate Japonica	767	85.80%	0.90%	0.00%	13.30%	NA
Tropical Japonica	504	8.90%	2.20%	1.19%	87.70%	NA
Japonica Intermediate	241	50.20%	2.10%	0.00%	47.72%	NA
VI/Aromatic	96	9.40%	1.00%	1.04%	88.54%	NA
Intermediate	90	22.20%	16.70%	3.33%	57.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1000213979	A -> G	LOC_Os10g01350.1	synonymous_variant ; p.Leu726Leu; LOW	synonymous_codon	Average:19.335; most accessible tissue: Zhenshan97 flag leaf, score: 51.466	N	N	N	N
vg1000213979	A -> DEL	LOC_Os10g01350.1	N	frameshift_variant	Average:19.335; most accessible tissue: Zhenshan97 flag leaf, score: 51.466	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1000213979	6.40E-06	8.11E-09	mr1532	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
vg1000213979	NA	4.89E-07	mr1781	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