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Detailed information for vg0127793554:

Variant ID: vg0127793554 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 27793554
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:

AAATACAGACACAAGCACAACTTCTTCGCAGGGGAATATCTAGTTTCAGTGTCCAAGAGCCGACGACTGAGATAAAATACAACTCGTTCTTTTCCATCCA[A/T]
CTCCTAAATCAATACTGAGCCGATTGACTTCTCACCAGCCGACAGATACAATATAAAAGGTATCCCTTTCTGTGGAGGAATCAAAACAGGAGGAGAGCTA

Reverse complement sequence

TAGCTCTCCTCCTGTTTTGATTCCTCCACAGAAAGGGATACCTTTTATATTGTATCTGTCGGCTGGTGAGAAGTCAATCGGCTCAGTATTGATTTAGGAG[T/A]
TGGATGGAAAAGAACGAGTTGTATTTTATCTCAGTCGTCGGCTCTTGGACACTGAAACTAGATATTCCCCTGCGAAGAAGTTGTGCTTGTGTCTGTATTT

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	96.50%	2.70%	0.85%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.04%	0.00%	NA
All Japonica	1512	89.70%	7.70%	2.51%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.40%	0.40%	0.22%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	81.20%	14.60%	4.17%	0.00%	NA
Tropical Japonica	504	99.20%	0.20%	0.60%	0.00%	NA
Japonica Intermediate	241	97.10%	1.70%	1.24%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	8.90%	1.11%	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
vg0127793554	A -> T	LOC_Os01g48480.1	downstream_gene_variant ; 2428.0bp to feature; MODIFIER	silent_mutation	Average:34.818; most accessible tissue: Minghui63 flag leaf, score: 59.244	N	N	N	N
vg0127793554	A -> T	LOC_Os01g48490.1	intron_variant ; MODIFIER	silent_mutation	Average:34.818; most accessible tissue: Minghui63 flag leaf, score: 59.244	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0127793554	4.34E-06	9.94E-09	mr1011_2	Jap_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