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Detailed information for vg1122327512:

Variant ID: vg1122327512 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 22327512
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGCACAATGGGTCCACCGTATATTAGTGAAAATTGACTGTCAGATGTTTTGTTTATTCTCATAATTTTTTATTTTTCTAATTTATTAAAATGCCAAGTAG[C/T]
GGTGTAGGAGCGTTTGTAGAAGTATTAAATGGCGGCTTGAGAGCGTTTATAGGATATTTAATGGACAAAGAGCTAAATATGCTTCCATATGATAATTTTT

Reverse complement sequence

AAAAATTATCATATGGAAGCATATTTAGCTCTTTGTCCATTAAATATCCTATAAACGCTCTCAAGCCGCCATTTAATACTTCTACAAACGCTCCTACACC[G/A]
CTACTTGGCATTTTAATAAATTAGAAAAATAAAAAATTATGAGAATAAACAAAACATCTGACAGTCAATTTTCACTAATATACGGTGGACCCATTGTGCT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	82.10%	1.50%	3.09%	13.33%	NA
All Indica	2759	76.50%	2.30%	4.75%	16.42%	NA
All Japonica	1512	89.50%	0.10%	0.53%	9.92%	NA
Aus	269	97.40%	0.00%	1.12%	1.49%	NA
Indica I	595	58.50%	2.00%	7.39%	32.10%	NA
Indica II	465	84.50%	1.70%	3.01%	10.75%	NA
Indica III	913	82.80%	3.10%	2.74%	11.39%	NA
Indica Intermediate	786	78.10%	2.00%	6.11%	13.74%	NA
Temperate Japonica	767	92.70%	0.10%	0.26%	6.91%	NA
Tropical Japonica	504	83.70%	0.00%	0.99%	15.28%	NA
Japonica Intermediate	241	91.30%	0.00%	0.41%	8.30%	NA
VI/Aromatic	96	89.60%	5.20%	1.04%	4.17%	NA
Intermediate	90	75.60%	0.00%	3.33%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1122327512	C -> T	LOC_Os11g37759.1	upstream_gene_variant ; 1455.0bp to feature; MODIFIER	silent_mutation	Average:17.162; most accessible tissue: Callus, score: 57.983	N	N	N	N
vg1122327512	C -> T	LOC_Os11g37759.3	upstream_gene_variant ; 1455.0bp to feature; MODIFIER	silent_mutation	Average:17.162; most accessible tissue: Callus, score: 57.983	N	N	N	N
vg1122327512	C -> T	LOC_Os11g37759.2	upstream_gene_variant ; 1455.0bp to feature; MODIFIER	silent_mutation	Average:17.162; most accessible tissue: Callus, score: 57.983	N	N	N	N
vg1122327512	C -> T	LOC_Os11g37750.1	downstream_gene_variant ; 2523.0bp to feature; MODIFIER	silent_mutation	Average:17.162; most accessible tissue: Callus, score: 57.983	N	N	N	N
vg1122327512	C -> T	LOC_Os11g37750-LOC_Os11g37759	intergenic_region ; MODIFIER	silent_mutation	Average:17.162; most accessible tissue: Callus, score: 57.983	N	N	N	N
vg1122327512	C -> DEL	N	N	silent_mutation	Average:17.162; most accessible tissue: Callus, score: 57.983	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1122327512	2.69E-06	NA	mr1974_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
vg1122327512	5.29E-06	3.19E-06	mr1974_2	Ind_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