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Detailed information for vg1108921957:

Variant ID: vg1108921957 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 8921957
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTCGTGCAGGACGAATTGGAAGGTAGGGTTTCCACAGGAAGCCCAAAGTTACAAGAAGCGCGATGCCTATAAGGCCAAGATGCGCCAGGAAATCATAGAT[T/C]
AAGTCACACAACAAGTCACCCAACAGTTCTATAGTCTTGCCACACAACATCCTCAAGCCTTCCCTGACCTGGTTCCTCAGGGATCGCAGTCGACGCAGAT

Reverse complement sequence

ATCTGCGTCGACTGCGATCCCTGAGGAACCAGGTCAGGGAAGGCTTGAGGATGTTGTGTGGCAAGACTATAGAACTGTTGGGTGACTTGTTGTGTGACTT[A/G]
ATCTATGATTTCCTGGCGCATCTTGGCCTTATAGGCATCGCGCTTCTTGTAACTTTGGGCTTCCTGTGGAAACCCTACCTTCCAATTCGTCCTGCACGAC

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	48.90%	0.90%	29.60%	20.57%	NA
All Indica	2759	21.10%	1.60%	43.57%	33.78%	NA
All Japonica	1512	90.60%	0.00%	8.13%	1.26%	NA
Aus	269	78.10%	0.00%	20.45%	1.49%	NA
Indica I	595	24.90%	0.70%	17.98%	56.47%	NA
Indica II	465	24.70%	1.10%	36.56%	37.63%	NA
Indica III	913	14.70%	2.60%	66.27%	16.43%	NA
Indica Intermediate	786	23.50%	1.30%	40.71%	34.48%	NA
Temperate Japonica	767	97.70%	0.00%	0.39%	1.96%	NA
Tropical Japonica	504	82.10%	0.00%	17.66%	0.20%	NA
Japonica Intermediate	241	85.90%	0.00%	12.86%	1.24%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	58.90%	1.10%	21.11%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1108921957	T -> DEL	N	N	silent_mutation	Average:32.544; most accessible tissue: Minghui63 young leaf, score: 66.656	N	N	N	N
vg1108921957	T -> C	LOC_Os11g15755.1	downstream_gene_variant ; 2716.0bp to feature; MODIFIER	silent_mutation	Average:32.544; most accessible tissue: Minghui63 young leaf, score: 66.656	N	N	N	N
vg1108921957	T -> C	LOC_Os11g15750.1	intron_variant ; MODIFIER	silent_mutation	Average:32.544; most accessible tissue: Minghui63 young leaf, score: 66.656	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1108921957	9.51E-07	1.54E-06	mr1268	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