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Detailed information for vg1106571584:

Variant ID: vg1106571584 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 6571584
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.86, C: 0.14, others allele: 0.00, population size: 42. )

Flanking Sequence (100 bp) in Reference Genome:

TCCCAACGCCGTTAGGCTGCGGCTGTTTCCGTTCTCCCTCCTCGGGAGAGCGAAGCAGTGGTTTTATGCCAACCGTGCTGCTATCAACACCTGGGATAAA[C/T]
GCTCTACGACATTCCTCTTGAAGTGCTTCCCGATGGGCAAAACCAACGCCCTTCGTGGACGAATTTCCAGTTTCCAGCAGACAAGGGACGAGTCCATTCC

Reverse complement sequence

GGAATGGACTCGTCCCTTGTCTGCTGGAAACTGGAAATTCGTCCACGAAGGGCGTTGGTTTTGCCCATCGGGAAGCACTTCAAGAGGAATGTCGTAGAGC[G/A]
TTTATCCCAGGTGTTGATAGCAGCACGGTTGGCATAAAACCACTGCTTCGCTCTCCCGAGGAGGGAGAACGGAAACAGCCGCAGCCTAACGGCGTTGGGA

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	36.80%	20.30%	1.67%	41.18%	NA
All Indica	2759	36.40%	7.10%	2.43%	54.04%	NA
All Japonica	1512	28.90%	47.00%	0.60%	23.48%	NA
Aus	269	73.60%	3.70%	0.00%	22.68%	NA
Indica I	595	21.30%	13.80%	1.34%	63.53%	NA
Indica II	465	23.90%	8.40%	4.30%	63.44%	NA
Indica III	913	52.90%	2.50%	1.86%	42.72%	NA
Indica Intermediate	786	36.10%	6.60%	2.80%	54.45%	NA
Temperate Japonica	767	23.90%	50.70%	0.78%	24.64%	NA
Tropical Japonica	504	38.50%	40.10%	0.40%	21.03%	NA
Japonica Intermediate	241	24.90%	49.80%	0.41%	24.90%	NA
VI/Aromatic	96	67.70%	19.80%	0.00%	12.50%	NA
Intermediate	90	38.90%	27.80%	3.33%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1106571584	C -> T	LOC_Os11g11830.1	upstream_gene_variant ; 2090.0bp to feature; MODIFIER	silent_mutation	Average:11.524; most accessible tissue: Zhenshan97 young leaf, score: 20.864	N	N	N	N
vg1106571584	C -> T	LOC_Os11g11840.1	upstream_gene_variant ; 338.0bp to feature; MODIFIER	silent_mutation	Average:11.524; most accessible tissue: Zhenshan97 young leaf, score: 20.864	N	N	N	N
vg1106571584	C -> T	LOC_Os11g11850.1	upstream_gene_variant ; 2699.0bp to feature; MODIFIER	silent_mutation	Average:11.524; most accessible tissue: Zhenshan97 young leaf, score: 20.864	N	N	N	N
vg1106571584	C -> T	LOC_Os11g11830-LOC_Os11g11840	intergenic_region ; MODIFIER	silent_mutation	Average:11.524; most accessible tissue: Zhenshan97 young leaf, score: 20.864	N	N	N	N
vg1106571584	C -> DEL	N	N	silent_mutation	Average:11.524; most accessible tissue: Zhenshan97 young leaf, score: 20.864	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1106571584	4.89E-06	NA	mr1977	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