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Detailed information for vg1109708668:

Variant ID: vg1109708668 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 9708668
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATAAGATAATTAGATTTTTAATATAAGATTATTATACTTAGCATATGTGAATGTTAGACTTAGCATATATCATTACTAAAATTTTAATATAAGATTATTA[G/A]
AGTTTACGTGGAGAGGGATGCGGAGGGGAACGAGGAGAGGAGGCTAGTGGAAGTCAACCCTCCGCTGGACAGAAGAGGGCACGCGGACAATGAGGTGCCG

Reverse complement sequence

CGGCACCTCATTGTCCGCGTGCCCTCTTCTGTCCAGCGGAGGGTTGACTTCCACTAGCCTCCTCTCCTCGTTCCCCTCCGCATCCCTCTCCACGTAAACT[C/T]
TAATAATCTTATATTAAAATTTTAGTAATGATATATGCTAAGTCTAACATTCACATATGCTAAGTATAATAATCTTATATTAAAAATCTAATTATCTTAT

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	92.00%	1.70%	0.55%	5.67%	NA
All Indica	2759	90.60%	0.00%	0.33%	9.03%	NA
All Japonica	1512	92.60%	5.40%	1.12%	0.93%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	93.60%	0.00%	0.00%	6.39%	NA
Indica II	465	88.80%	0.00%	0.22%	10.97%	NA
Indica III	913	94.70%	0.00%	0.11%	5.15%	NA
Indica Intermediate	786	84.70%	0.00%	0.89%	14.38%	NA
Temperate Japonica	767	90.70%	5.90%	1.56%	1.83%	NA
Tropical Japonica	504	99.00%	0.60%	0.40%	0.00%	NA
Japonica Intermediate	241	85.10%	13.70%	1.24%	0.00%	NA
VI/Aromatic	96	96.90%	1.00%	0.00%	2.08%	NA
Intermediate	90	96.70%	0.00%	0.00%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1109708668	G -> A	LOC_Os11g17410.1	upstream_gene_variant ; 625.0bp to feature; MODIFIER	silent_mutation	Average:33.808; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg1109708668	G -> A	LOC_Os11g17420.1	upstream_gene_variant ; 4530.0bp to feature; MODIFIER	silent_mutation	Average:33.808; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg1109708668	G -> A	LOC_Os11g17400.1	downstream_gene_variant ; 2263.0bp to feature; MODIFIER	silent_mutation	Average:33.808; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg1109708668	G -> A	LOC_Os11g17400-LOC_Os11g17410	intergenic_region ; MODIFIER	silent_mutation	Average:33.808; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg1109708668	G -> DEL	N	N	silent_mutation	Average:33.808; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1109708668	2.73E-09	2.73E-09	mr1191_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