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Detailed information for vg0919357146:

Variant ID: vg0919357146 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 19357146
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTTACTGAGTACACTTCTAGACAGCACTATTTTGATTGTGCCTGTCAAATGTGCGTTCCTGAAGATTTTGTTTCTAATTAATTTGTGCTTGTTAATTGT[G/A]
CGTTCCTGAAGATTTTGTTTCTAATTAATTTGTGCCTGTCAAATGTGCGTTCCTGAAGATTTTGTTTCTGCTTGATTTGTGCCTGTCAAATGTGTGTTCC

Reverse complement sequence

GGAACACACATTTGACAGGCACAAATCAAGCAGAAACAAAATCTTCAGGAACGCACATTTGACAGGCACAAATTAATTAGAAACAAAATCTTCAGGAACG[C/T]
ACAATTAACAAGCACAAATTAATTAGAAACAAAATCTTCAGGAACGCACATTTGACAGGCACAATCAAAATAGTGCTGTCTAGAAGTGTACTCAGTAAAT

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	60.80%	13.80%	18.66%	6.79%	NA
All Indica	2759	33.50%	23.40%	31.64%	11.42%	NA
All Japonica	1512	99.90%	0.10%	0.07%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	71.60%	5.90%	21.51%	1.01%	NA
Indica II	465	16.60%	24.30%	33.33%	25.81%	NA
Indica III	913	16.30%	37.70%	34.72%	11.28%	NA
Indica Intermediate	786	34.70%	19.60%	34.73%	10.94%	NA
Temperate Japonica	767	99.70%	0.10%	0.13%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	82.20%	2.20%	8.89%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0919357146	G -> DEL	N	N	silent_mutation	Average:58.144; most accessible tissue: Callus, score: 74.79	N	N	N	N
vg0919357146	G -> A	LOC_Os09g32410.1	upstream_gene_variant ; 87.0bp to feature; MODIFIER	silent_mutation	Average:58.144; most accessible tissue: Callus, score: 74.79	N	N	N	N
vg0919357146	G -> A	LOC_Os09g32430.1	downstream_gene_variant ; 771.0bp to feature; MODIFIER	silent_mutation	Average:58.144; most accessible tissue: Callus, score: 74.79	N	N	N	N
vg0919357146	G -> A	LOC_Os09g32410-LOC_Os09g32430	intergenic_region ; MODIFIER	silent_mutation	Average:58.144; most accessible tissue: Callus, score: 74.79	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0919357146	NA	7.30E-08	mr1279	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