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Detailed information for vg0910719144:

Variant ID: vg0910719144 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 10719144
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TACTAGAAGTCCTAATCCTCCTAGGAAACCTTCTCATACAAGAAATAATCTTTACATAACCAATCATACCAAATTTGGACTCTTTTCCAAATTCGACTCC[G/A]
TATCCCATACGCACACAATACCTCCATCGTATGCCATATGGAATCTTCACCAACCACGTATATTGAACTCTAGCCTAAGTATCCCGTATGATATCTGACC

Reverse complement sequence

GGTCAGATATCATACGGGATACTTAGGCTAGAGTTCAATATACGTGGTTGGTGAAGATTCCATATGGCATACGATGGAGGTATTGTGTGCGTATGGGATA[C/T]
GGAGTCGAATTTGGAAAAGAGTCCAAATTTGGTATGATTGGTTATGTAAAGATTATTTCTTGTATGAGAAGGTTTCCTAGGAGGATTAGGACTTCTAGTA

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	22.40%	5.90%	0.91%	70.78%	NA
All Indica	2759	14.00%	9.90%	1.38%	74.77%	NA
All Japonica	1512	27.80%	0.20%	0.13%	71.89%	NA
Aus	269	77.00%	0.00%	0.00%	23.05%	NA
Indica I	595	12.10%	0.00%	0.84%	87.06%	NA
Indica II	465	13.80%	12.30%	1.72%	72.26%	NA
Indica III	913	16.90%	16.30%	0.99%	65.83%	NA
Indica Intermediate	786	12.10%	8.50%	2.04%	77.35%	NA
Temperate Japonica	767	47.10%	0.10%	0.13%	52.67%	NA
Tropical Japonica	504	6.20%	0.20%	0.20%	93.45%	NA
Japonica Intermediate	241	11.60%	0.40%	0.00%	87.97%	NA
VI/Aromatic	96	26.00%	1.00%	0.00%	72.92%	NA
Intermediate	90	23.30%	3.30%	3.33%	70.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0910719144	G -> DEL	N	N	silent_mutation	Average:9.253; most accessible tissue: Callus, score: 24.272	N	N	N	N
vg0910719144	G -> A	LOC_Os09g17520.1	intron_variant ; MODIFIER	silent_mutation	Average:9.253; most accessible tissue: Callus, score: 24.272	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0910719144	4.34E-06	3.85E-07	mr1696	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