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Detailed information for vg0612772228:

Variant ID: vg0612772228 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 12772228
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCCCAGTGTATTTAGCATACATAATTTAGCATCGCTAAACAGAGGGAATTAGCAAGATTAATTTTTTAAAATTAATCTACTAATCTCGTAGATATATCCG[A/G]
CATATATCTACACAGGTACGCAATGTTTTATACAATTTACCGTACTCGTTTTTCAGATAAATATAATATTATTAGATCCATAATTTATTATATTTACCTA

Reverse complement sequence

TAGGTAAATATAATAAATTATGGATCTAATAATATTATATTTATCTGAAAAACGAGTACGGTAAATTGTATAAAACATTGCGTACCTGTGTAGATATATG[T/C]
CGGATATATCTACGAGATTAGTAGATTAATTTTAAAAAATTAATCTTGCTAATTCCCTCTGTTTAGCGATGCTAAATTATGTATGCTAAATACACTGGGA

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	92.50%	1.90%	5.59%	0.00%	NA
All Indica	2759	99.80%	0.00%	0.14%	0.00%	NA
All Japonica	1512	77.20%	5.80%	17.00%	0.00%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	99.30%	0.20%	0.50%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.00%	0.13%	0.00%	NA
Temperate Japonica	767	62.50%	9.50%	28.03%	0.00%	NA
Tropical Japonica	504	94.40%	2.60%	2.98%	0.00%	NA
Japonica Intermediate	241	88.00%	0.80%	11.20%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	2.20%	2.22%	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
vg0612772228	A -> G	LOC_Os06g22040.1	upstream_gene_variant ; 1050.0bp to feature; MODIFIER	silent_mutation	Average:60.721; most accessible tissue: Minghui63 flag leaf, score: 70.648	N	N	N	N
vg0612772228	A -> G	LOC_Os06g22030-LOC_Os06g22040	intergenic_region ; MODIFIER	silent_mutation	Average:60.721; most accessible tissue: Minghui63 flag leaf, score: 70.648	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0612772228	NA	6.19E-06	mr1379_2	Jap_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