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Detailed information for vg0920808559:

Variant ID: vg0920808559 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 20808559
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGTCGACAACAGTTAGATAGGCTACCCCAAATATTGTACTGGTGTGATTATGGTGAATAAGAGCAATATCGGCTTCGGCCAACAGGATGTAGGGTTATTA[C/A]
CTGACAATTCAGGGGCCCGAACCTGTATAAAATTCCTCGCCTCCGTCTCTTTTACCTTAGTCTCGCATATACCTTAGTACCAACAATCCCCATACTATGC

Reverse complement sequence

GCATAGTATGGGGATTGTTGGTACTAAGGTATATGCGAGACTAAGGTAAAAGAGACGGAGGCGAGGAATTTTATACAGGTTCGGGCCCCTGAATTGTCAG[G/T]
TAATAACCCTACATCCTGTTGGCCGAAGCCGATATTGCTCTTATTCACCATAATCACACCAGTACAATATTTGGGGTAGCCTATCTAACTGTTGTCGACA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	42.30%	8.80%	1.63%	47.23%	NA
All Indica	2759	12.20%	6.00%	2.61%	79.16%	NA
All Japonica	1512	99.40%	0.40%	0.13%	0.07%	NA
Aus	269	3.00%	86.60%	0.37%	10.04%	NA
Indica I	595	11.10%	3.00%	1.68%	84.20%	NA
Indica II	465	8.60%	8.80%	3.23%	79.35%	NA
Indica III	913	12.20%	4.10%	2.63%	81.16%	NA
Indica Intermediate	786	15.30%	8.90%	2.93%	72.90%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	96.70%	2.50%	0.41%	0.41%	NA
VI/Aromatic	96	90.60%	4.20%	2.08%	3.12%	NA
Intermediate	90	72.20%	8.90%	0.00%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0920808559	C -> DEL	N	N	silent_mutation	Average:20.308; most accessible tissue: Zhenshan97 panicle, score: 46.362	N	N	N	N
vg0920808559	C -> A	LOC_Os09g36140.1	downstream_gene_variant ; 2807.0bp to feature; MODIFIER	silent_mutation	Average:20.308; most accessible tissue: Zhenshan97 panicle, score: 46.362	N	N	N	N
vg0920808559	C -> A	LOC_Os09g36130-LOC_Os09g36140	intergenic_region ; MODIFIER	silent_mutation	Average:20.308; most accessible tissue: Zhenshan97 panicle, score: 46.362	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0920808559	3.90E-06	NA	mr1261	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
vg0920808559	NA	2.14E-07	mr1803	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
vg0920808559	NA	1.48E-06	mr1929_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