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Detailed information for vg1127185490:

Variant ID: vg1127185490 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 27185490
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 124. )

Flanking Sequence (100 bp) in Reference Genome:

ATGGATGTGACACATCCTAGTACAATGAATCTGGACAAACCATATGTACAGATTCATTGTACTAGGATGTGCCACATCTACCCAAAATCTCTTATATTAT[G/A]
GAACGGAGGGAGTATCATATTTGTGTGGTCGCACTAACAGAGGTTTGTGATGCTTATGCTTATATTTATATGCCAAAATTTAAATTTTTGACCTTAAATT

Reverse complement sequence

AATTTAAGGTCAAAAATTTAAATTTTGGCATATAAATATAAGCATAAGCATCACAAACCTCTGTTAGTGCGACCACACAAATATGATACTCCCTCCGTTC[C/T]
ATAATATAAGAGATTTTGGGTAGATGTGGCACATCCTAGTACAATGAATCTGTACATATGGTTTGTCCAGATTCATTGTACTAGGATGTGTCACATCCAT

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	77.30%	13.50%	0.63%	8.55%	NA
All Indica	2759	72.50%	16.20%	0.91%	10.40%	NA
All Japonica	1512	86.70%	6.70%	0.33%	6.22%	NA
Aus	269	90.00%	6.70%	0.00%	3.35%	NA
Indica I	595	23.20%	55.50%	1.18%	20.17%	NA
Indica II	465	80.40%	3.00%	1.51%	15.05%	NA
Indica III	913	93.50%	1.40%	0.55%	4.49%	NA
Indica Intermediate	786	80.70%	11.50%	0.76%	7.12%	NA
Temperate Japonica	767	92.00%	6.10%	0.00%	1.83%	NA
Tropical Japonica	504	80.60%	5.40%	0.60%	13.49%	NA
Japonica Intermediate	241	82.60%	11.60%	0.83%	4.98%	NA
VI/Aromatic	96	35.40%	62.50%	0.00%	2.08%	NA
Intermediate	90	74.40%	12.20%	0.00%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1127185490	G -> A	LOC_Os11g44910.1	upstream_gene_variant ; 1431.0bp to feature; MODIFIER	silent_mutation	Average:48.217; most accessible tissue: Zhenshan97 panicle, score: 79.799	N	N	N	N
vg1127185490	G -> A	LOC_Os11g44910.2	upstream_gene_variant ; 1442.0bp to feature; MODIFIER	silent_mutation	Average:48.217; most accessible tissue: Zhenshan97 panicle, score: 79.799	N	N	N	N
vg1127185490	G -> A	LOC_Os11g44910.3	upstream_gene_variant ; 1442.0bp to feature; MODIFIER	silent_mutation	Average:48.217; most accessible tissue: Zhenshan97 panicle, score: 79.799	N	N	N	N
vg1127185490	G -> A	LOC_Os11g44910-LOC_Os11g44920	intergenic_region ; MODIFIER	silent_mutation	Average:48.217; most accessible tissue: Zhenshan97 panicle, score: 79.799	N	N	N	N
vg1127185490	G -> DEL	N	N	silent_mutation	Average:48.217; most accessible tissue: Zhenshan97 panicle, score: 79.799	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1127185490	4.67E-07	4.67E-07	mr1674	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