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Detailed information for vg1102499895:

Variant ID: vg1102499895 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 2499895
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATTTTTTTCTGCTGTGAGTGTGTTTAGTTTATGCCAAAATTGAAAGTTTGGTTGAAATTGAAACGATGTGACAGAAAAATTAAAAGTTTGTATGTGTAG[G/A]
AAAGTTTTGATATGATGGAAAAGTTGGAAGTTCGAAGAAAAAAATTGAAACTAAACTCGGCCTATATCAAATATTAAACCTTACACCATCAAATCAAGTC

Reverse complement sequence

GACTTGATTTGATGGTGTAAGGTTTAATATTTGATATAGGCCGAGTTTAGTTTCAATTTTTTTCTTCGAACTTCCAACTTTTCCATCATATCAAAACTTT[C/T]
CTACACATACAAACTTTTAATTTTTCTGTCACATCGTTTCAATTTCAACCAAACTTTCAATTTTGGCATAAACTAAACACACTCACAGCAGAAAAAAATT

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	86.50%	12.40%	0.97%	0.17%	NA
All Indica	2759	86.20%	13.10%	0.51%	0.25%	NA
All Japonica	1512	88.40%	10.40%	1.19%	0.00%	NA
Aus	269	80.70%	16.40%	2.97%	0.00%	NA
Indica I	595	99.20%	0.70%	0.17%	0.00%	NA
Indica II	465	96.80%	3.00%	0.22%	0.00%	NA
Indica III	913	73.60%	25.00%	0.77%	0.66%	NA
Indica Intermediate	786	84.60%	14.60%	0.64%	0.13%	NA
Temperate Japonica	767	99.00%	0.70%	0.39%	0.00%	NA
Tropical Japonica	504	69.40%	28.20%	2.38%	0.00%	NA
Japonica Intermediate	241	94.20%	4.60%	1.24%	0.00%	NA
VI/Aromatic	96	85.40%	9.40%	5.21%	0.00%	NA
Intermediate	90	84.40%	13.30%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1102499895	G -> A	LOC_Os11g05540.1	upstream_gene_variant ; 537.0bp to feature; MODIFIER	silent_mutation	Average:47.118; most accessible tissue: Minghui63 flower, score: 68.171	N	N	N	N
vg1102499895	G -> A	LOC_Os11g05530-LOC_Os11g05540	intergenic_region ; MODIFIER	silent_mutation	Average:47.118; most accessible tissue: Minghui63 flower, score: 68.171	N	N	N	N
vg1102499895	G -> DEL	N	N	silent_mutation	Average:47.118; most accessible tissue: Minghui63 flower, score: 68.171	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1102499895	1.84E-06	2.59E-07	mr1622	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