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Detailed information for vg0128855514:

Variant ID: vg0128855514 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 28855514
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:

CACTATGTTTTCCACTTAGACAAACAACTGCAACAGAGGTCTTTCACTGCATACACATAGACATAAAAACAATAACTTTTAATCTATTAACACACTCAAC[T/A]
TAGATATAGATGGAAACCTAACTCGTCACCTGTCACACAATCATGTATTGGCATAATGTAGGGCGGCGGTGCTGCAGATCTACAGGATGGCGTTGTAGGG

Reverse complement sequence

CCCTACAACGCCATCCTGTAGATCTGCAGCACCGCCGCCCTACATTATGCCAATACATGATTGTGTGACAGGTGACGAGTTAGGTTTCCATCTATATCTA[A/T]
GTTGAGTGTGTTAATAGATTAAAAGTTATTGTTTTTATGTCTATGTGTATGCAGTGAAAGACCTCTGTTGCAGTTGTTTGTCTAAGTGGAAAACATAGTG

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	96.10%	2.60%	1.25%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.04%	0.00%	NA
All Japonica	1512	88.60%	7.80%	3.57%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.40%	0.60%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.00%	0.13%	0.00%	NA
Temperate Japonica	767	89.00%	5.70%	5.22%	0.00%	NA
Tropical Japonica	504	92.90%	6.20%	0.99%	0.00%	NA
Japonica Intermediate	241	78.40%	17.80%	3.73%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	2.20%	4.44%	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
vg0128855514	T -> A	LOC_Os01g50220.1	intron_variant ; MODIFIER	silent_mutation	Average:55.889; most accessible tissue: Minghui63 root, score: 65.279	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0128855514	NA	4.87E-06	mr1720	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
vg0128855514	NA	1.33E-06	mr1549_2	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
vg0128855514	NA	7.00E-06	mr1757_2	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