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Detailed information for vg0510321290:

Variant ID: vg0510321290 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 10321290
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.06, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:

TCCCGGGCAGGCGTTCCAGTTCGGCAGCCTCAACTTCATCACCAACGACTTCGGCAAGATCTCTCTCCTTGACTCGGACTCAAACCAGTCGGGGAGAGAC[C/T]
AGGTCCCCGTGGCATTCGGTATTCCGAACTCGGCCGAGGCCTACTCCAAGATCATCTCTCCCGAGTCGGCTTCAAACCACTCGGACGAGATCCAATCTAC

Reverse complement sequence

GTAGATTGGATCTCGTCCGAGTGGTTTGAAGCCGACTCGGGAGAGATGATCTTGGAGTAGGCCTCGGCCGAGTTCGGAATACCGAATGCCACGGGGACCT[G/A]
GTCTCTCCCCGACTGGTTTGAGTCCGAGTCAAGGAGAGAGATCTTGCCGAAGTCGTTGGTGATGAAGTTGAGGCTGCCGAACTGGAACGCCTGCCCGGGA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	90.20%	9.60%	0.17%	0.00%	NA
All Indica	2759	91.40%	8.50%	0.11%	0.00%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	21.60%	76.60%	1.86%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	98.90%	1.10%	0.00%	0.00%	NA
Indica III	913	82.10%	17.70%	0.11%	0.00%	NA
Indica Intermediate	786	91.20%	8.50%	0.25%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	10.00%	0.00%	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
vg0510321290	C -> T	LOC_Os05g17960.1	stop_gained ; p.Gln47*; HIGH	stop_gained	Average:45.827; most accessible tissue: Zhenshan97 flag leaf, score: 75.761	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0510321290	NA	1.75E-12	mr1610_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
vg0510321290	4.46E-06	NA	mr1629_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