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Detailed information for vg1123045587:

Variant ID: vg1123045587 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 23045587
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.01, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:

GAATTTCGATTTGTGTTTACTTAGGTTTCGGCGAGTGAACGGCGGTTAGACCGGTGATTGACGATCAAACCGGAGCTACTACACCAGTTAGACTGGTGGC[T/C]
TCTAGGTGGTCAGACCTGCATCAACTCCGGTCAGACCGATCTTCATCGATTCAAGGGAATCTTTTAATTCATCTATAAGTTTTGGTTTTGGAGTACTACA

Reverse complement sequence

TGTAGTACTCCAAAACCAAAACTTATAGATGAATTAAAAGATTCCCTTGAATCGATGAAGATCGGTCTGACCGGAGTTGATGCAGGTCTGACCACCTAGA[A/G]
GCCACCAGTCTAACTGGTGTAGTAGCTCCGGTTTGATCGTCAATCACCGGTCTAACCGCCGTTCACTCGCCGAAACCTAAGTAAACACAAATCGAAATTC

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	67.60%	21.80%	0.40%	10.18%	NA
All Indica	2759	52.30%	33.60%	0.51%	13.56%	NA
All Japonica	1512	93.10%	5.20%	0.00%	1.72%	NA
Aus	269	75.50%	0.40%	1.12%	23.05%	NA
Indica I	595	54.60%	32.80%	0.84%	11.76%	NA
Indica II	465	68.40%	29.00%	0.00%	2.58%	NA
Indica III	913	43.80%	30.80%	0.44%	24.97%	NA
Indica Intermediate	786	51.00%	40.20%	0.64%	8.14%	NA
Temperate Japonica	767	94.80%	2.90%	0.00%	2.35%	NA
Tropical Japonica	504	94.80%	4.00%	0.00%	1.19%	NA
Japonica Intermediate	241	83.80%	15.40%	0.00%	0.83%	NA
VI/Aromatic	96	81.20%	6.20%	0.00%	12.50%	NA
Intermediate	90	72.20%	17.80%	2.22%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1123045587	T -> DEL	N	N	silent_mutation	Average:41.138; most accessible tissue: Zhenshan97 young leaf, score: 66.32	N	N	N	N
vg1123045587	T -> C	LOC_Os11g38760-LOC_Os11g38765	intergenic_region ; MODIFIER	silent_mutation	Average:41.138; most accessible tissue: Zhenshan97 young leaf, score: 66.32	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1123045587	NA	5.82E-06	mr1170	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