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Detailed information for vg1101198038:

Variant ID: vg1101198038 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 1198038
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCGAGCCATGAAGTTAAGCATGAAACGACCCCCGTACAACCGCACTTCTCGTATGGGTATAGACCTAGTGGAGTAGATAGCCGAGCGAGGCAGTATCCCT[G/A]
CATAGATGATTCACCCCTGAGTGAGGCAGGTGCGCTACGGTGGGACAGCCGTTGAGGTAGGGCCGAGAGGCGTGCCCTACATCGGTGTCGCCATTGGTAG

Reverse complement sequence

CTACCAATGGCGACACCGATGTAGGGCACGCCTCTCGGCCCTACCTCAACGGCTGTCCCACCGTAGCGCACCTGCCTCACTCAGGGGTGAATCATCTATG[C/T]
AGGGATACTGCCTCGCTCGGCTATCTACTCCACTAGGTCTATACCCATACGAGAAGTGCGGTTGTACGGGGGTCGTTTCATGCTTAACTTCATGGCTCGG

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	36.00%	4.90%	13.29%	45.83%	NA
All Indica	2759	8.40%	0.30%	19.46%	71.84%	NA
All Japonica	1512	83.30%	14.40%	0.33%	1.92%	NA
Aus	269	31.60%	0.00%	24.91%	43.49%	NA
Indica I	595	4.90%	0.00%	12.94%	82.18%	NA
Indica II	465	16.60%	0.60%	11.83%	70.97%	NA
Indica III	913	4.20%	0.00%	28.04%	67.80%	NA
Indica Intermediate	786	11.20%	0.60%	18.96%	69.21%	NA
Temperate Japonica	767	92.00%	5.90%	0.39%	1.69%	NA
Tropical Japonica	504	71.20%	26.60%	0.20%	1.98%	NA
Japonica Intermediate	241	80.90%	16.20%	0.41%	2.49%	NA
VI/Aromatic	96	81.20%	0.00%	8.33%	10.42%	NA
Intermediate	90	48.90%	7.80%	12.22%	31.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1101198038	G -> A	LOC_Os11g03260.1	upstream_gene_variant ; 207.0bp to feature; MODIFIER	silent_mutation	Average:22.263; most accessible tissue: Minghui63 flag leaf, score: 45.195	N	N	N	N
vg1101198038	G -> A	LOC_Os11g03270.1	upstream_gene_variant ; 4702.0bp to feature; MODIFIER	silent_mutation	Average:22.263; most accessible tissue: Minghui63 flag leaf, score: 45.195	N	N	N	N
vg1101198038	G -> A	LOC_Os11g03250.1	downstream_gene_variant ; 3074.0bp to feature; MODIFIER	silent_mutation	Average:22.263; most accessible tissue: Minghui63 flag leaf, score: 45.195	N	N	N	N
vg1101198038	G -> A	LOC_Os11g03260-LOC_Os11g03270	intergenic_region ; MODIFIER	silent_mutation	Average:22.263; most accessible tissue: Minghui63 flag leaf, score: 45.195	N	N	N	N
vg1101198038	G -> DEL	N	N	silent_mutation	Average:22.263; most accessible tissue: Minghui63 flag leaf, score: 45.195	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1101198038	3.39E-07	NA	mr1204	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