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Detailed information for vg1105886395:

Variant ID: vg1105886395 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 5886395
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATGTTCTTTTTATTAACACAGTAAAAACACAGATGCCCGCGCACACTCACTTTTATGAATACACACACGCATATTTTATCTATATGAGCACCTTTCAAA[G/C]
ACTATGTCTTGAGATTAATGAATTCGCCACAAGCGACTCGTTGTCGATGAATATGTATGAATATGTACCTCCCACTGAAAAAAATTAACTTTGAGTACTT

Reverse complement sequence

AAGTACTCAAAGTTAATTTTTTTCAGTGGGAGGTACATATTCATACATATTCATCGACAACGAGTCGCTTGTGGCGAATTCATTAATCTCAAGACATAGT[C/G]
TTTGAAAGGTGCTCATATAGATAAAATATGCGTGTGTGTATTCATAAAAGTGAGTGTGCGCGGGCATCTGTGTTTTTACTGTGTTAATAAAAAGAACATT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	95.20%	1.00%	2.39%	1.48%	NA
All Indica	2759	97.90%	0.00%	1.01%	1.05%	NA
All Japonica	1512	96.60%	3.00%	0.40%	0.00%	NA
Aus	269	59.90%	0.00%	25.28%	14.87%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.00%	0.00%	0.22%	NA
Indica III	913	95.40%	0.00%	2.74%	1.86%	NA
Indica Intermediate	786	98.20%	0.00%	0.38%	1.40%	NA
Temperate Japonica	767	96.60%	3.40%	0.00%	0.00%	NA
Tropical Japonica	504	98.60%	0.60%	0.79%	0.00%	NA
Japonica Intermediate	241	92.10%	7.10%	0.83%	0.00%	NA
VI/Aromatic	96	89.60%	0.00%	9.38%	1.04%	NA
Intermediate	90	97.80%	0.00%	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
vg1105886395	G -> DEL	N	N	silent_mutation	Average:78.883; most accessible tissue: Minghui63 root, score: 87.964	N	N	N	N
vg1105886395	G -> C	LOC_Os11g10720.1	upstream_gene_variant ; 3146.0bp to feature; MODIFIER	silent_mutation	Average:78.883; most accessible tissue: Minghui63 root, score: 87.964	N	N	N	N
vg1105886395	G -> C	LOC_Os11g10710-LOC_Os11g10720	intergenic_region ; MODIFIER	silent_mutation	Average:78.883; most accessible tissue: Minghui63 root, score: 87.964	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1105886395	3.96E-08	7.30E-07	mr1613_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