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Detailed information for vg1122792828:

Variant ID: vg1122792828 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 22792828
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.71, C: 0.29, others allele: 0.00, population size: 38. )

Flanking Sequence (100 bp) in Reference Genome:

GTGGCAAAGCGAGAGAGCAGGAAAATAGAATTAGTGGGGATGACTTGTATATGTATATAGGATTCGGGGCTTGTTCACTTTGCTACCATTTTCAACCTTA[T/C]
CAAGTTTTGGCAAAGTTACCAAAAAAGTGGCTACATTTAGTTTGTTGCTAAATTTTAGTAACTACATATGAAATCTTTGCCAAAATTTGACAATCTTACC

Reverse complement sequence

GGTAAGATTGTCAAATTTTGGCAAAGATTTCATATGTAGTTACTAAAATTTAGCAACAAACTAAATGTAGCCACTTTTTTGGTAACTTTGCCAAAACTTG[A/G]
TAAGGTTGAAAATGGTAGCAAAGTGAACAAGCCCCGAATCCTATATACATATACAAGTCATCCCCACTAATTCTATTTTCCTGCTCTCTCGCTTTGCCAC

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	39.80%	6.90%	0.89%	52.41%	NA
All Indica	2759	41.10%	2.80%	1.27%	54.80%	NA
All Japonica	1512	43.10%	15.30%	0.33%	41.27%	NA
Aus	269	15.60%	0.00%	0.74%	83.64%	NA
Indica I	595	18.80%	0.20%	2.02%	78.99%	NA
Indica II	465	64.30%	1.50%	0.86%	33.33%	NA
Indica III	913	35.50%	5.70%	1.31%	57.50%	NA
Indica Intermediate	786	50.90%	2.20%	0.89%	46.06%	NA
Temperate Japonica	767	47.80%	19.70%	0.26%	32.20%	NA
Tropical Japonica	504	47.20%	12.90%	0.20%	39.68%	NA
Japonica Intermediate	241	19.50%	6.20%	0.83%	73.44%	NA
VI/Aromatic	96	3.10%	10.40%	0.00%	86.46%	NA
Intermediate	90	54.40%	8.90%	0.00%	36.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1122792828	T -> DEL	N	N	silent_mutation	Average:44.806; most accessible tissue: Minghui63 root, score: 82.818	N	N	N	N
vg1122792828	T -> C	LOC_Os11g38470.1	downstream_gene_variant ; 2166.0bp to feature; MODIFIER	silent_mutation	Average:44.806; most accessible tissue: Minghui63 root, score: 82.818	N	N	N	N
vg1122792828	T -> C	LOC_Os11g38462-LOC_Os11g38470	intergenic_region ; MODIFIER	silent_mutation	Average:44.806; most accessible tissue: Minghui63 root, score: 82.818	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1122792828	5.82E-06	NA	mr1124	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