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Detailed information for vg0610693135:

Variant ID: vg0610693135 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 10693135
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 331. )

Flanking Sequence (100 bp) in Reference Genome:

TTCGGTTTGCTTGATTCAGCTGACCTTCCTGGCACCAATGCACTTCGTTTACTCGGACTGGTTGTCTCCAAAGAAGAATCATTCTGAGAACACAGTTTCA[G/A]
TGACTGTAAGTTGGGAGCTGCAGGGGGCGCTCGAGGCATTGCCTTTGAAGCCATTGCTCCCACAACTGATACGTATATATATCAGACCAGATTGCAGAAA

Reverse complement sequence

TTTCTGCAATCTGGTCTGATATATATACGTATCAGTTGTGGGAGCAATGGCTTCAAAGGCAATGCCTCGAGCGCCCCCTGCAGCTCCCAACTTACAGTCA[C/T]
TGAAACTGTGTTCTCAGAATGATTCTTCTTTGGAGACAACCAGTCCGAGTAAACGAAGTGCATTGGTGCCAGGAAGGTCAGCTGAATCAAGCAAACCGAA

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	92.50%	5.20%	2.24%	0.00%	NA
All Indica	2759	99.80%	0.00%	0.14%	0.00%	NA
All Japonica	1512	77.40%	16.10%	6.48%	0.00%	NA
Aus	269	99.30%	0.00%	0.74%	0.00%	NA
Indica I	595	99.30%	0.00%	0.67%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	65.40%	24.30%	10.30%	0.00%	NA
Tropical Japonica	504	94.80%	3.80%	1.39%	0.00%	NA
Japonica Intermediate	241	79.30%	15.80%	4.98%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	95.60%	3.30%	1.11%	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
vg0610693135	G -> A	LOC_Os06g18830.1	synonymous_variant ; p.Leu19Leu; LOW	synonymous_codon	Average:64.477; most accessible tissue: Zhenshan97 young leaf, score: 76.773	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0610693135	3.47E-07	NA	mr1087_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
vg0610693135	3.16E-06	NA	mr1087_2	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