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Detailed information for vg0128139083:

Variant ID: vg0128139083 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 28139083
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, A: 0.03, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

CTAATATTCCTTACTCCCTCCGTCCCAAAAAAAGACAAATCCTGGTTTCCGTGTCCAACGTTTGACCGTCCGTCTTATTTGGAAAAATTATGAAAAAAAA[T/A]
TAAAAAGACAAGTCACGCATAAAATATTAATCATGTTTTATCATCTAACAACAATGAAAATACGAATTATAAAAAAATTTCATATAAGACGGACAGTCAA

Reverse complement sequence

TTGACTGTCCGTCTTATATGAAATTTTTTTATAATTCGTATTTTCATTGTTGTTAGATGATAAAACATGATTAATATTTTATGCGTGACTTGTCTTTTTA[A/T]
TTTTTTTTCATAATTTTTCCAAATAAGACGGACGGTCAAACGTTGGACACGGAAACCAGGATTTGTCTTTTTTTGGGACGGAGGGAGTAAGGAATATTAG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	54.30%	45.30%	0.32%	0.06%	NA
All Indica	2759	30.50%	68.90%	0.54%	0.11%	NA
All Japonica	1512	87.40%	12.60%	0.00%	0.00%	NA
Aus	269	91.80%	8.20%	0.00%	0.00%	NA
Indica I	595	34.60%	64.20%	1.18%	0.00%	NA
Indica II	465	58.90%	40.20%	0.65%	0.22%	NA
Indica III	913	6.50%	93.20%	0.22%	0.11%	NA
Indica Intermediate	786	38.40%	61.10%	0.38%	0.13%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	64.50%	35.50%	0.00%	0.00%	NA
Japonica Intermediate	241	96.30%	3.70%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	68.90%	31.10%	0.00%	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
vg0128139083	T -> A	LOC_Os01g49000.1	intron_variant ; MODIFIER	silent_mutation	Average:23.893; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg0128139083	T -> DEL	N	N	silent_mutation	Average:23.893; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0128139083	NA	8.65E-06	mr1596	Jap_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
vg0128139083	1.90E-06	2.40E-10	mr1550_2	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