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Detailed information for vg1111258291:

Variant ID: vg1111258291 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 11258291
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, C: 0.00, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

TAACATAATCAATTGACAAACAAATCATTCTTCAAGATCAGGATGCACATCAGTCTTGCCATCTGCAGGAAGAGGGAAAGCAGAAGAGCCAGGCATGGCT[T/C]
GTGACTGTGGAGAAGCAAGCCAAGCAGTCGGTGGCAGTGAGAACCAGAGACCTCCATATGGATACGGCGCTGCCTGCGGCGTCGGAACAGCGAGAGGACC

Reverse complement sequence

GGTCCTCTCGCTGTTCCGACGCCGCAGGCAGCGCCGTATCCATATGGAGGTCTCTGGTTCTCACTGCCACCGACTGCTTGGCTTGCTTCTCCACAGTCAC[A/G]
AGCCATGCCTGGCTCTTCTGCTTTCCCTCTTCCTGCAGATGGCAAGACTGATGTGCATCCTGATCTTGAAGAATGATTTGTTTGTCAATTGATTATGTTA

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	61.50%	27.80%	0.30%	10.43%	NA
All Indica	2759	37.60%	44.90%	0.47%	17.04%	NA
All Japonica	1512	95.60%	3.50%	0.07%	0.86%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	11.60%	64.20%	0.50%	23.70%	NA
Indica II	465	58.90%	39.80%	0.43%	0.86%	NA
Indica III	913	40.60%	34.00%	0.22%	25.19%	NA
Indica Intermediate	786	41.20%	45.90%	0.76%	12.09%	NA
Temperate Japonica	767	96.90%	2.20%	0.13%	0.78%	NA
Tropical Japonica	504	92.50%	6.70%	0.00%	0.79%	NA
Japonica Intermediate	241	97.90%	0.80%	0.00%	1.24%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	68.90%	20.00%	0.00%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1111258291	T -> DEL	LOC_Os11g19530.1	N	frameshift_variant	Average:73.375; most accessible tissue: Zhenshan97 panicle, score: 88.625	N	N	N	N
vg1111258291	T -> C	LOC_Os11g19530.1	missense_variant ; p.Gln54Arg; MODERATE	nonsynonymous_codon ; Q54R	Average:73.375; most accessible tissue: Zhenshan97 panicle, score: 88.625	benign	0.708	DELETERIOUS	0.03

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1111258291	NA	6.46E-07	mr1154_2	Ind_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