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Detailed information for vg0906569206:

Variant ID: vg0906569206 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 6569206
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.61, G: 0.39, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:

TATTGAAACTCGTCAAGAACATTCTTCCGGAGGGAAACAAATTGCCCGAGACAACGTATGAGGCTAAGAAGATAGTCTGCCCTCTAGGACTGGAAGTTCA[A/G]
AAGATTCACGCATGTCCGAATGATTGTATCCTATATCGCGGTGACTAGTACGAGAACCTAGAAGCATGCCCTGTTTGCAAAGCACTACGATACAAGATTA

Reverse complement sequence

TAATCTTGTATCGTAGTGCTTTGCAAACAGGGCATGCTTCTAGGTTCTCGTACTAGTCACCGCGATATAGGATACAATCATTCGGACATGCGTGAATCTT[T/C]
TGAACTTCCAGTCCTAGAGGGCAGACTATCTTCTTAGCCTCATACGTTGTCTCGGGCAATTTGTTTCCCTCCGGAAGAATGTTCTTGACGAGTTTCAATA

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	44.00%	37.10%	18.98%	0.00%	NA
All Indica	2759	44.50%	28.20%	27.29%	0.00%	NA
All Japonica	1512	46.40%	52.10%	1.52%	0.00%	NA
Aus	269	24.50%	49.10%	26.39%	0.00%	NA
Indica I	595	52.60%	25.90%	21.51%	0.00%	NA
Indica II	465	33.30%	28.20%	38.49%	0.00%	NA
Indica III	913	47.80%	26.90%	25.30%	0.00%	NA
Indica Intermediate	786	41.30%	31.30%	27.35%	0.00%	NA
Temperate Japonica	767	11.20%	88.30%	0.52%	0.00%	NA
Tropical Japonica	504	85.30%	11.70%	2.98%	0.00%	NA
Japonica Intermediate	241	77.20%	21.20%	1.66%	0.00%	NA
VI/Aromatic	96	42.70%	19.80%	37.50%	0.00%	NA
Intermediate	90	44.40%	40.00%	15.56%	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
vg0906569206	A -> G	LOC_Os09g11750.1	splice_region_variant&intron_variant ; LOW	silent_mutation	Average:23.207; most accessible tissue: Minghui63 flag leaf, score: 53.617	N	N	N	N
vg0906569206	A -> G	LOC_Os09g11760.1	downstream_gene_variant ; 4179.0bp to feature; MODIFIER	silent_mutation	Average:23.207; most accessible tissue: Minghui63 flag leaf, score: 53.617	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0906569206	1.08E-06	4.94E-07	mr1350	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