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Detailed information for vg1126179984:

Variant ID: vg1126179984 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 26179984
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.57, T: 0.43, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:

GGCGTCGGTGGTGACTGGTGAGCAGTGGATGGAATGGAAGGCATGGACATGTTGTTTATGAATTTCTGGACTGAAGCATCCAGAACGCAGTGTTTACACC[C/T]
AAATTTGGCACTTAGGATTAAAATAGGAAATATTGCTAAAATTTGGAAGTCTACCGGTTTCCTCCGAGGTAGGCCGGTCTGACCGCCGTGTGTTGGGCGG

Reverse complement sequence

CCGCCCAACACACGGCGGTCAGACCGGCCTACCTCGGAGGAAACCGGTAGACTTCCAAATTTTAGCAATATTTCCTATTTTAATCCTAAGTGCCAAATTT[G/A]
GGTGTAAACACTGCGTTCTGGATGCTTCAGTCCAGAAATTCATAAACAACATGTCCATGCCTTCCATTCCATCCACTGCTCACCAGTCACCACCGACGCC

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	29.90%	25.60%	0.76%	43.74%	NA
All Indica	2759	13.70%	26.90%	0.94%	58.54%	NA
All Japonica	1512	65.10%	20.00%	0.46%	14.35%	NA
Aus	269	1.50%	42.00%	1.12%	55.39%	NA
Indica I	595	7.90%	21.00%	0.67%	70.42%	NA
Indica II	465	6.70%	62.40%	1.94%	29.03%	NA
Indica III	913	22.50%	7.70%	0.55%	69.33%	NA
Indica Intermediate	786	12.00%	32.60%	1.02%	54.45%	NA
Temperate Japonica	767	64.30%	32.30%	0.65%	2.74%	NA
Tropical Japonica	504	71.40%	3.60%	0.20%	24.80%	NA
Japonica Intermediate	241	54.80%	15.40%	0.41%	29.46%	NA
VI/Aromatic	96	19.80%	32.30%	0.00%	47.92%	NA
Intermediate	90	30.00%	25.60%	0.00%	44.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1126179984	C -> T	LOC_Os11g43370.1	upstream_gene_variant ; 1442.0bp to feature; MODIFIER	silent_mutation	Average:50.483; most accessible tissue: Minghui63 panicle, score: 85.069	N	N	N	N
vg1126179984	C -> T	LOC_Os11g43360-LOC_Os11g43370	intergenic_region ; MODIFIER	silent_mutation	Average:50.483; most accessible tissue: Minghui63 panicle, score: 85.069	N	N	N	N
vg1126179984	C -> DEL	N	N	silent_mutation	Average:50.483; most accessible tissue: Minghui63 panicle, score: 85.069	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1126179984	2.65E-06	3.58E-08	mr1668	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