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Detailed information for vg0906665147:

Variant ID: vg0906665147 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 6665147
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCATATGAAAAATGAAAAAATAGTCATCGGTGACGGGCATTAGTTAATGCCCAATAGAGATTAAGTGTATAGCCCGTCACTGATGAGTCATCTGTGACGG[G/A]
CCTAGTTGTTATCTCAAACGGGCCTCAAGTTGATGCACGTCACGGATGATGGTCATCCGTGATGGGCCACAACTTGAGGCCCGTTTGAGATATGGAATGT

Reverse complement sequence

ACATTCCATATCTCAAACGGGCCTCAAGTTGTGGCCCATCACGGATGACCATCATCCGTGACGTGCATCAACTTGAGGCCCGTTTGAGATAACAACTAGG[C/T]
CCGTCACAGATGACTCATCAGTGACGGGCTATACACTTAATCTCTATTGGGCATTAACTAATGCCCGTCACCGATGACTATTTTTTCATTTTTCATATGA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	98.00%	1.20%	0.78%	0.00%	NA
All Indica	2759	96.70%	1.90%	1.34%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.20%	1.00%	0.84%	0.00%	NA
Indica II	465	93.80%	4.50%	1.72%	0.00%	NA
Indica III	913	99.70%	0.00%	0.33%	0.00%	NA
Indica Intermediate	786	94.00%	3.30%	2.67%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	2.20%	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
vg0906665147	G -> A	LOC_Os09g11880.1	upstream_gene_variant ; 596.0bp to feature; MODIFIER	silent_mutation	Average:38.848; most accessible tissue: Minghui63 root, score: 68.289	N	N	N	N
vg0906665147	G -> A	LOC_Os09g11870-LOC_Os09g11880	intergenic_region ; MODIFIER	silent_mutation	Average:38.848; most accessible tissue: Minghui63 root, score: 68.289	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0906665147	3.30E-06	NA	mr1020_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