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Detailed information for vg0619891832:

Variant ID: vg0619891832 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 19891832
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:

CTAATGGGCAGGTCGAGGCATCTAACAAAAGCTTGATCAAATTGATTAAGCGGAAGATTTCTGATTATCCTCGGCAATGGCATACTCGGTTGGCCGAAGC[G/A]
TTGTGGTCTTATCGGATGGCTTGTCATGGATCGATCCAAGTCCCTCCTTACAAACTTGTTTATGGACATGAGGCTGTTCTACCACGGGAAGTTAGAATCG

Reverse complement sequence

CGATTCTAACTTCCCGTGGTAGAACAGCCTCATGTCCATAAACAAGTTTGTAAGGAGGGACTTGGATCGATCCATGACAAGCCATCCGATAAGACCACAA[C/T]
GCTTCGGCCAACCGAGTATGCCATTGCCGAGGATAATCAGAAATCTTCCGCTTAATCAATTTGATCAAGCTTTTGTTAGATGCCTCGACCTGCCCATTAG

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	37.60%	33.10%	4.44%	24.82%	NA
All Indica	2759	61.90%	3.50%	3.15%	31.46%	NA
All Japonica	1512	0.50%	93.80%	0.53%	5.16%	NA
Aus	269	9.70%	0.40%	26.39%	63.57%	NA
Indica I	595	49.70%	3.00%	3.87%	43.36%	NA
Indica II	465	71.00%	4.10%	1.29%	23.66%	NA
Indica III	913	68.50%	1.20%	2.85%	27.49%	NA
Indica Intermediate	786	58.00%	6.20%	4.07%	31.68%	NA
Temperate Japonica	767	0.50%	97.00%	0.00%	2.48%	NA
Tropical Japonica	504	0.40%	88.50%	0.79%	10.32%	NA
Japonica Intermediate	241	0.80%	94.60%	1.66%	2.90%	NA
VI/Aromatic	96	16.70%	3.10%	41.67%	38.54%	NA
Intermediate	90	24.40%	50.00%	4.44%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0619891832	G -> A	LOC_Os06g34140.1	synonymous_variant ; p.Ala1507Ala; LOW	synonymous_codon	Average:12.648; most accessible tissue: Zhenshan97 flag leaf, score: 18.943	N	N	N	N
vg0619891832	G -> DEL	LOC_Os06g34140.1	N	frameshift_variant	Average:12.648; most accessible tissue: Zhenshan97 flag leaf, score: 18.943	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0619891832	3.29E-06	NA	mr1693	Ind_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