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Detailed information for vg1112967711:

Variant ID: vg1112967711 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 12967711
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGTCATGCGTTGGATAATTATTCTCATGAGGGCGTAACTGCCTAGATGCATAGGCAACCACCTTCCCATCTTGCATCAAAACACAACCCAAACCATGTCT[A/G]
GATGCATCACAATACACCTAAAAACCTTTCCTTGGATCAGGCAAGACTAACACTGGCACAGTCACTAGCCTTTTCTTCAATTCTTGAAAACTCTGCTCAC

Reverse complement sequence

GTGAGCAGAGTTTTCAAGAATTGAAGAAAAGGCTAGTGACTGTGCCAGTGTTAGTCTTGCCTGATCCAAGGAAAGGTTTTTAGGTGTATTGTGATGCATC[T/C]
AGACATGGTTTGGGTTGTGTTTTGATGCAAGATGGGAAGGTGGTTGCCTATGCATCTAGGCAGTTACGCCCTCATGAGAATAATTATCCAACGCATGACC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	95.90%	0.10%	0.87%	3.07%	NA
All Indica	2759	94.10%	0.20%	1.09%	4.60%	NA
All Japonica	1512	98.50%	0.10%	0.66%	0.79%	NA
Aus	269	99.60%	0.00%	0.00%	0.37%	NA
Indica I	595	99.00%	0.00%	0.17%	0.84%	NA
Indica II	465	94.00%	0.00%	0.22%	5.81%	NA
Indica III	913	88.10%	0.50%	2.41%	8.98%	NA
Indica Intermediate	786	97.60%	0.00%	0.76%	1.65%	NA
Temperate Japonica	767	99.70%	0.00%	0.26%	0.00%	NA
Tropical Japonica	504	96.80%	0.20%	1.39%	1.59%	NA
Japonica Intermediate	241	97.90%	0.00%	0.41%	1.66%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	94.40%	0.00%	0.00%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1112967711	A -> DEL	N	N	silent_mutation	Average:14.545; most accessible tissue: Callus, score: 34.244	N	N	N	N
vg1112967711	A -> G	LOC_Os11g22560.1	downstream_gene_variant ; 3265.0bp to feature; MODIFIER	silent_mutation	Average:14.545; most accessible tissue: Callus, score: 34.244	N	N	N	N
vg1112967711	A -> G	LOC_Os11g22550.1	intron_variant ; MODIFIER	silent_mutation	Average:14.545; most accessible tissue: Callus, score: 34.244	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1112967711	3.77E-06	NA	mr1371_2	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
vg1112967711	6.95E-06	3.24E-06	mr1371_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1112967711	NA	5.52E-06	mr1977_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251