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Detailed information for vg1211114784:

Variant ID: vg1211114784 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 11114784
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGCTGTCTTGTTGAAGTTGGTTTTGTCGCTGCCGTCAAGGATTGCCTGTGGAGTGGAGTCGCCTGCTGCTGAAGTCAAGCTTCCCAGTTTAGCTCGCTTT[A/T]
ATCTTTCCCGCTGCATTTGTAATCTTTTATATTTTTGTAAGACGTGGGTCTGTATGTCAACAATTGTCGTTTGTGTACCCTGGCTGGTCCTGGACAGGGG

Reverse complement sequence

CCCCTGTCCAGGACCAGCCAGGGTACACAAACGACAATTGTTGACATACAGACCCACGTCTTACAAAAATATAAAAGATTACAAATGCAGCGGGAAAGAT[T/A]
AAAGCGAGCTAAACTGGGAAGCTTGACTTCAGCAGCAGGCGACTCCACTCCACAGGCAATCCTTGACGGCAGCGACAAAACCAACTTCAACAAGACAGCT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	88.80%	0.10%	4.02%	7.09%	NA
All Indica	2759	92.70%	0.00%	3.59%	3.66%	NA
All Japonica	1512	79.20%	0.10%	5.49%	15.28%	NA
Aus	269	98.50%	0.00%	0.37%	1.12%	NA
Indica I	595	91.30%	0.00%	5.21%	3.53%	NA
Indica II	465	90.10%	0.00%	4.52%	5.38%	NA
Indica III	913	95.40%	0.10%	2.41%	2.08%	NA
Indica Intermediate	786	92.20%	0.00%	3.18%	4.58%	NA
Temperate Japonica	767	86.70%	0.10%	3.13%	10.04%	NA
Tropical Japonica	504	77.20%	0.00%	5.75%	17.06%	NA
Japonica Intermediate	241	59.30%	0.00%	12.45%	28.22%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	1.10%	7.78%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1211114784	A -> DEL	N	N	silent_mutation	Average:14.476; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N
vg1211114784	A -> T	LOC_Os12g19140.1	upstream_gene_variant ; 1688.0bp to feature; MODIFIER	silent_mutation	Average:14.476; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N
vg1211114784	A -> T	LOC_Os12g19150.1	upstream_gene_variant ; 951.0bp to feature; MODIFIER	silent_mutation	Average:14.476; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N
vg1211114784	A -> T	LOC_Os12g19140-LOC_Os12g19150	intergenic_region ; MODIFIER	silent_mutation	Average:14.476; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1211114784	NA	5.29E-16	mr1158	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