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Detailed information for vg1122796698:

Variant ID: vg1122796698 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 22796698
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTTTGTATGAAAAAGTTACGTATATATACATGTTTTTTCAAAAAAATTGATCCTTGTCTACGGATATCGAAAAAAATCCAGATAATTTCCAACTGTTTTC[T/C]
GATTCCAACGGATAGTGTCCTTATTGTGTTTGTTTTTGTTTCCAAAAAAAAAAACAAATTCGTTTTTGAATCCAAAAATATGCGGAACTGTGTTCAACTG

Reverse complement sequence

CAGTTGAACACAGTTCCGCATATTTTTGGATTCAAAAACGAATTTGTTTTTTTTTTTGGAAACAAAAACAAACACAATAAGGACACTATCCGTTGGAATC[A/G]
GAAAACAGTTGGAAATTATCTGGATTTTTTTCGATATCCGTAGACAAGGATCAATTTTTTTGAAAAAACATGTATATATACGTAACTTTTTCATACAAAG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	47.20%	5.00%	0.68%	47.08%	NA
All Indica	2759	44.90%	0.10%	0.98%	54.04%	NA
All Japonica	1512	58.50%	15.30%	0.13%	26.06%	NA
Aus	269	16.40%	0.00%	0.74%	82.90%	NA
Indica I	595	20.00%	0.00%	1.18%	78.82%	NA
Indica II	465	66.70%	0.20%	2.37%	30.75%	NA
Indica III	913	42.90%	0.00%	0.44%	56.63%	NA
Indica Intermediate	786	53.10%	0.30%	0.64%	46.06%	NA
Temperate Japonica	767	68.20%	4.60%	0.26%	26.99%	NA
Tropical Japonica	504	59.70%	20.00%	0.00%	20.24%	NA
Japonica Intermediate	241	24.90%	39.80%	0.00%	35.27%	NA
VI/Aromatic	96	8.30%	0.00%	1.04%	90.62%	NA
Intermediate	90	64.40%	2.20%	0.00%	33.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1122796698	T -> DEL	N	N	silent_mutation	Average:19.371; most accessible tissue: Callus, score: 63.555	N	N	N	N
vg1122796698	T -> C	LOC_Os11g38470.1	upstream_gene_variant ; 1036.0bp to feature; MODIFIER	silent_mutation	Average:19.371; most accessible tissue: Callus, score: 63.555	N	N	N	N
vg1122796698	T -> C	LOC_Os11g38480.1	upstream_gene_variant ; 2590.0bp to feature; MODIFIER	silent_mutation	Average:19.371; most accessible tissue: Callus, score: 63.555	N	N	N	N
vg1122796698	T -> C	LOC_Os11g38470-LOC_Os11g38480	intergenic_region ; MODIFIER	silent_mutation	Average:19.371; most accessible tissue: Callus, score: 63.555	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1122796698	5.65E-06	NA	mr1580	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
vg1122796698	4.49E-08	1.48E-08	mr1766	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
vg1122796698	9.07E-06	NA	mr1825	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