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Detailed information for vg1122072549:

Variant ID: vg1122072549 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 22072549
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.71, T: 0.30, others allele: 0.00, population size: 182. )

Flanking Sequence (100 bp) in Reference Genome:

AAGTATCACTCAATCACTCAACGATGTTTCCTCTATCCCATAAAAAACCAACTTAGCACTGTCCAAATTTATAGAGGAAAAATATATATGAAAGGCTATG[C/T]
ATGCATGGTAGTAGGTCTAGATAAGGGAACAACCAACCCCTCGAAATGGCATTGGCAACTAGCTGCTACACAAAGCTAGAATTTCCGGTACCTATTCTAG

Reverse complement sequence

CTAGAATAGGTACCGGAAATTCTAGCTTTGTGTAGCAGCTAGTTGCCAATGCCATTTCGAGGGGTTGGTTGTTCCCTTATCTAGACCTACTACCATGCAT[G/A]
CATAGCCTTTCATATATATTTTTCCTCTATAAATTTGGACAGTGCTAAGTTGGTTTTTTATGGGATAGAGGAAACATCGTTGAGTGATTGAGTGATACTT

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	55.20%	39.10%	0.42%	5.31%	NA
All Indica	2759	69.60%	25.60%	0.51%	4.31%	NA
All Japonica	1512	29.60%	67.70%	0.20%	2.51%	NA
Aus	269	67.30%	6.30%	0.74%	25.65%	NA
Indica I	595	76.30%	23.20%	0.17%	0.34%	NA
Indica II	465	66.90%	30.80%	1.08%	1.29%	NA
Indica III	913	69.90%	21.80%	0.44%	7.89%	NA
Indica Intermediate	786	65.80%	28.80%	0.51%	4.96%	NA
Temperate Japonica	767	14.30%	84.90%	0.26%	0.52%	NA
Tropical Japonica	504	43.10%	51.60%	0.00%	5.36%	NA
Japonica Intermediate	241	50.20%	46.50%	0.41%	2.90%	NA
VI/Aromatic	96	12.50%	67.70%	0.00%	19.79%	NA
Intermediate	90	52.20%	40.00%	1.11%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1122072549	C -> T	LOC_Os11g37390.1	downstream_gene_variant ; 2140.0bp to feature; MODIFIER	silent_mutation	Average:63.609; most accessible tissue: Callus, score: 87.74	N	N	N	N
vg1122072549	C -> T	LOC_Os11g37390-LOC_Os11g37400	intergenic_region ; MODIFIER	silent_mutation	Average:63.609; most accessible tissue: Callus, score: 87.74	N	N	N	N
vg1122072549	C -> DEL	N	N	silent_mutation	Average:63.609; most accessible tissue: Callus, score: 87.74	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1122072549	NA	8.14E-09	mr1544	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
vg1122072549	NA	6.81E-06	mr1159_2	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
vg1122072549	NA	7.69E-09	mr1624_2	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