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Detailed information for vg0907533269:

Variant ID: vg0907533269 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 7533269
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTTTAACTTTTATTGATCTTAACTGAGTTTCATTATTACAAACTGAAGACTCTCACACCACCAAACTCACCAACTTCCTAACACTCAAAAACAAACAAAC[A/G]
CATGCACTTACATCCCACCACTGATGTAAATCACATGCGAGACACCCACAAGCAAACTTAAAACAAGCAAACTAACACAACGATCTAAGACAACGGTTAG

Reverse complement sequence

CTAACCGTTGTCTTAGATCGTTGTGTTAGTTTGCTTGTTTTAAGTTTGCTTGTGGGTGTCTCGCATGTGATTTACATCAGTGGTGGGATGTAAGTGCATG[T/C]
GTTTGTTTGTTTTTGAGTGTTAGGAAGTTGGTGAGTTTGGTGGTGTGAGAGTCTTCAGTTTGTAATAATGAAACTCAGTTAAGATCAATAAAAGTTAAAG

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	39.50%	0.90%	29.05%	30.58%	NA
All Indica	2759	12.80%	1.40%	44.73%	40.99%	NA
All Japonica	1512	87.30%	0.00%	0.99%	11.71%	NA
Aus	269	15.60%	0.70%	42.01%	41.64%	NA
Indica I	595	15.60%	0.80%	31.26%	52.27%	NA
Indica II	465	7.30%	1.10%	32.69%	58.92%	NA
Indica III	913	11.30%	2.10%	62.32%	24.32%	NA
Indica Intermediate	786	15.80%	1.40%	41.60%	41.22%	NA
Temperate Japonica	767	77.40%	0.00%	1.30%	21.25%	NA
Tropical Japonica	504	98.60%	0.00%	0.60%	0.79%	NA
Japonica Intermediate	241	95.00%	0.00%	0.83%	4.15%	NA
VI/Aromatic	96	94.80%	0.00%	2.08%	3.12%	NA
Intermediate	90	65.60%	0.00%	10.00%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0907533269	A -> G	LOC_Os09g13060.1	upstream_gene_variant ; 1295.0bp to feature; MODIFIER	silent_mutation	Average:11.678; most accessible tissue: Minghui63 young leaf, score: 24.836	N	N	N	N
vg0907533269	A -> G	LOC_Os09g13080.1	downstream_gene_variant ; 3553.0bp to feature; MODIFIER	silent_mutation	Average:11.678; most accessible tissue: Minghui63 young leaf, score: 24.836	N	N	N	N
vg0907533269	A -> G	LOC_Os09g13070.1	intron_variant ; MODIFIER	silent_mutation	Average:11.678; most accessible tissue: Minghui63 young leaf, score: 24.836	N	N	N	N
vg0907533269	A -> DEL	N	N	silent_mutation	Average:11.678; most accessible tissue: Minghui63 young leaf, score: 24.836	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0907533269	3.52E-06	NA	mr1248	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