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Detailed information for vg0911755343:

Variant ID: vg0911755343 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 11755343
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

ATGCTACTTATCTCACATGATGTCTTGGATGTTGTGTAGAAACCATGTCTCATGCAAGACATGGTTTCCTTCTCTTTCCTTATTTATTCACTTGCCACAT[C/T]
ATTTTTCATCTTAGGTGACAGCTTATTTAATACTATGGACATCATCCTAGTCATTGGGTTGGGAATGGCCTTATACACTTCGCTCTTGACAGCTCTCGCC

Reverse complement sequence

GGCGAGAGCTGTCAAGAGCGAAGTGTATAAGGCCATTCCCAACCCAATGACTAGGATGATGTCCATAGTATTAAATAAGCTGTCACCTAAGATGAAAAAT[G/A]
ATGTGGCAAGTGAATAAATAAGGAAAGAGAAGGAAACCATGTCTTGCATGAGACATGGTTTCTACACAACATCCAAGACATCATGTGAGATAAGTAGCAT

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	88.50%	11.20%	0.11%	0.23%	NA
All Indica	2759	80.80%	18.70%	0.11%	0.40%	NA
All Japonica	1512	99.30%	0.50%	0.13%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	85.70%	14.30%	0.00%	0.00%	NA
Indica II	465	82.40%	17.40%	0.00%	0.22%	NA
Indica III	913	79.50%	20.30%	0.11%	0.11%	NA
Indica Intermediate	786	77.60%	21.00%	0.25%	1.15%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	98.60%	1.00%	0.40%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	96.70%	3.30%	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
vg0911755343	C -> DEL	N	N	silent_mutation	Average:65.367; most accessible tissue: Zhenshan97 panicle, score: 84.374	N	N	N	N
vg0911755343	C -> T	LOC_Os09g19650-LOC_Os09g19670	intergenic_region ; MODIFIER	silent_mutation	Average:65.367; most accessible tissue: Zhenshan97 panicle, score: 84.374	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0911755343	NA	1.50E-06	mr1689	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