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Detailed information for vg0909037704:

Variant ID: vg0909037704 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 9037704
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCTCCAGATTCAGCCTTATGCCTGCTGTGCGCAAGCTGTCGAATGTCTCCTGCAGGTCGATCGCATGGTCGAAAGCCTTGCGGCTTTTTACGACTATGTC[G/A]
TCGACGTAAGCTTCCACATTCCGCCCCAACTGCTTGCCAAGGACCTTGTACACCAACCTGGCGAAAGTTGCTCCTGCGTTCCTTAAGCCAAAAGGCATCC

Reverse complement sequence

GGATGCCTTTTGGCTTAAGGAACGCAGGAGCAACTTTCGCCAGGTTGGTGTACAAGGTCCTTGGCAAGCAGTTGGGGCGGAATGTGGAAGCTTACGTCGA[C/T]
GACATAGTCGTAAAAAGCCGCAAGGCTTTCGACCATGCGATCGACCTGCAGGAGACATTCGACAGCTTGCGCACAGCAGGCATAAGGCTGAATCTGGAGA

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	76.60%	2.00%	21.16%	0.28%	NA
All Indica	2759	68.10%	2.60%	28.89%	0.47%	NA
All Japonica	1512	95.00%	0.30%	4.76%	0.00%	NA
Aus	269	57.60%	7.10%	35.32%	0.00%	NA
Indica I	595	62.40%	1.80%	35.13%	0.67%	NA
Indica II	465	63.20%	2.20%	34.19%	0.43%	NA
Indica III	913	77.40%	3.80%	18.40%	0.33%	NA
Indica Intermediate	786	64.40%	1.90%	33.21%	0.51%	NA
Temperate Japonica	767	95.40%	0.00%	4.56%	0.00%	NA
Tropical Japonica	504	99.20%	0.20%	0.60%	0.00%	NA
Japonica Intermediate	241	84.60%	1.20%	14.11%	0.00%	NA
VI/Aromatic	96	77.10%	0.00%	22.92%	0.00%	NA
Intermediate	90	84.40%	0.00%	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
vg0909037704	G -> DEL	LOC_Os09g15010.1	N	frameshift_variant	Average:12.901; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0909037704	G -> A	LOC_Os09g15010.1	synonymous_variant ; p.Asp864Asp; LOW	synonymous_codon	Average:12.901; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0909037704	NA	4.35E-08	mr1299_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0909037704	1.12E-06	NA	mr1486_2	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
vg0909037704	2.32E-06	NA	mr1486_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0909037704	NA	2.53E-10	mr1595_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0909037704	NA	4.06E-08	mr1727_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0909037704	NA	1.43E-06	mr1785_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0909037704	NA	3.18E-06	mr1840_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251