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Detailed information for vg0509795936:

Variant ID: vg0509795936 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 9795936
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAACCGCAAGCCAGCGTGGGCAACGGCTTTACTTTCTGTATAGTATGGTTCATAGTAGAGCACCAGACTGTGAAGTGGCGGAGATAAGCCCACGGGGGTC[A/G]
CTGGGGAGTCCATACCTTGTTTATAAGGGGGTGATTATGATCCGGGAACGGTGCACTGCTTTGAACAGTATTATACAGAGGGTATTGTCACAATCTCTAT

Reverse complement sequence

ATAGAGATTGTGACAATACCCTCTGTATAATACTGTTCAAAGCAGTGCACCGTTCCCGGATCATAATCACCCCCTTATAAACAAGGTATGGACTCCCCAG[T/C]
GACCCCCGTGGGCTTATCTCCGCCACTTCACAGTCTGGTGCTCTACTATGAACCATACTATACAGAAAGTAAAGCCGTTGCCCACGCTGGCTTGCGGTTG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	89.30%	10.20%	0.57%	0.00%	NA
All Indica	2759	88.70%	10.50%	0.76%	0.00%	NA
All Japonica	1512	99.30%	0.60%	0.07%	0.00%	NA
Aus	269	34.60%	63.60%	1.86%	0.00%	NA
Indica I	595	92.10%	7.90%	0.00%	0.00%	NA
Indica II	465	99.10%	0.90%	0.00%	0.00%	NA
Indica III	913	79.30%	18.90%	1.75%	0.00%	NA
Indica Intermediate	786	90.80%	8.50%	0.64%	0.00%	NA
Temperate Japonica	767	99.30%	0.50%	0.13%	0.00%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	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
vg0509795936	A -> G	LOC_Os05g17120.1	intron_variant ; MODIFIER	silent_mutation	Average:52.99; most accessible tissue: Minghui63 flag leaf, score: 73.334	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0509795936	NA	7.19E-06	mr1331	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
vg0509795936	NA	8.60E-11	mr1499	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
vg0509795936	4.00E-06	NA	mr1274_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