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Detailed information for vg0909177526:

Variant ID: vg0909177526 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 9177526
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACGACAACCGCGACCTTGACGACTTCGACGAAAGCTTTGAAGATAACTACACCCCTCTCTATTTTGGCGTCTTCATGGCCGATAACGAGACGGAAGAACA[G/A]
CGCCAAGCCCGAGAAGCAGAAGGACGACGTGTACAACAGGAGGCCGAACGACGCCGACTGGAAGAGGAGCGCCAGGCACAAGAGCAAGAACGGCTGCAGC

Reverse complement sequence

GCTGCAGCCGTTCTTGCTCTTGTGCCTGGCGCTCCTCTTCCAGTCGGCGTCGTTCGGCCTCCTGTTGTACACGTCGTCCTTCTGCTTCTCGGGCTTGGCG[C/T]
TGTTCTTCCGTCTCGTTATCGGCCATGAAGACGCCAAAATAGAGAGGGGTGTAGTTATCTTCAAAGCTTTCGTCGAAGTCGTCAAGGTCGCGGTTGTCGT

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	38.80%	34.90%	15.28%	11.00%	NA
All Indica	2759	58.90%	10.60%	21.57%	8.92%	NA
All Japonica	1512	2.70%	77.60%	4.76%	14.88%	NA
Aus	269	53.50%	34.90%	10.78%	0.74%	NA
Indica I	595	49.10%	9.60%	29.92%	11.43%	NA
Indica II	465	55.70%	10.10%	23.87%	10.32%	NA
Indica III	913	68.30%	11.40%	14.24%	6.02%	NA
Indica Intermediate	786	57.30%	10.80%	22.39%	9.54%	NA
Temperate Japonica	767	0.70%	75.60%	4.69%	19.04%	NA
Tropical Japonica	504	5.80%	85.10%	6.35%	2.78%	NA
Japonica Intermediate	241	2.90%	68.50%	1.66%	26.97%	NA
VI/Aromatic	96	5.20%	32.30%	18.75%	43.75%	NA
Intermediate	90	22.20%	63.30%	8.89%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0909177526	G -> DEL	LOC_Os09g15120.1	N	frameshift_variant	Average:25.109; most accessible tissue: Callus, score: 39.182	N	N	N	N
vg0909177526	G -> A	LOC_Os09g15120.1	synonymous_variant ; p.Gln146Gln; LOW	synonymous_codon	Average:25.109; most accessible tissue: Callus, score: 39.182	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0909177526	NA	9.02E-07	mr1836_2	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