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Detailed information for vg0922359301:

Variant ID: vg0922359301 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 22359301
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, T: 0.01, others allele: 0.00, population size: 81. )

Flanking Sequence (100 bp) in Reference Genome:

TACAAGTTAGCGACTAATTTAACAAGTGTGTATTACTTACCTCGTCGTAATTCGCACAATATTTCCCATTAACCCTTAGGAACTCAGAACAATAATATCC[G/T]
CATAGTACTATTCCCACCGGTTGCTTGTGACACTTTCAACATCAAAATAATTATAAGGTATAATAAGTTATTACATGGAAACACACAAGCATTTATGAAA

Reverse complement sequence

TTTCATAAATGCTTGTGTGTTTCCATGTAATAACTTATTATACCTTATAATTATTTTGATGTTGAAAGTGTCACAAGCAACCGGTGGGAATAGTACTATG[C/A]
GGATATTATTGTTCTGAGTTCCTAAGGGTTAATGGGAAATATTGTGCGAATTACGACGAGGTAAGTAATACACACTTGTTAAATTAGTCGCTAACTTGTA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	53.60%	22.00%	2.26%	22.20%	NA
All Indica	2759	26.20%	36.90%	2.39%	34.51%	NA
All Japonica	1512	99.40%	0.20%	0.07%	0.33%	NA
Aus	269	54.60%	2.60%	13.75%	29.00%	NA
Indica I	595	17.50%	76.00%	0.50%	6.05%	NA
Indica II	465	12.70%	42.60%	2.37%	42.37%	NA
Indica III	913	35.80%	10.60%	2.74%	50.82%	NA
Indica Intermediate	786	29.50%	34.60%	3.44%	32.44%	NA
Temperate Japonica	767	99.90%	0.00%	0.00%	0.13%	NA
Tropical Japonica	504	99.00%	0.20%	0.00%	0.79%	NA
Japonica Intermediate	241	98.80%	0.80%	0.41%	0.00%	NA
VI/Aromatic	96	97.90%	0.00%	1.04%	1.04%	NA
Intermediate	90	73.30%	10.00%	2.22%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0922359301	G -> DEL	LOC_Os09g38940.1	N	frameshift_variant	Average:13.702; most accessible tissue: Callus, score: 22.371	N	N	N	N
vg0922359301	G -> T	LOC_Os09g38940.1	stop_gained ; p.Cys301*; HIGH	stop_gained	Average:13.702; most accessible tissue: Callus, score: 22.371	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0922359301	NA	8.64E-06	mr1019_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
vg0922359301	7.54E-06	1.81E-06	mr1036_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
vg0922359301	NA	2.96E-06	mr1051_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
vg0922359301	9.34E-06	1.39E-06	mr1169_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
vg0922359301	NA	2.79E-06	mr1968_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