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Detailed information for vg0419549428:

Variant ID: vg0419549428 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 19549428
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:

GCTATATATATATAAATTATGTAGGATTTGTAAAAGAACCTATACATGATATCCATTACCACCTCTAATCGTGCTCAAGCTCAATCTTGATCTTTTCGAA[T/G]
GAACTAATGAAGGACAAAGTGTCATATATGAATAATCCTTAATTTAATTATTTTCTTCTCTCGATAGATCGATCAATCTGCCTAGATCTCTTTCAAGTAC

Reverse complement sequence

GTACTTGAAAGAGATCTAGGCAGATTGATCGATCTATCGAGAGAAGAAAATAATTAAATTAAGGATTATTCATATATGACACTTTGTCCTTCATTAGTTC[A/C]
TTCGAAAAGATCAAGATTGAGCTTGAGCACGATTAGAGGTGGTAATGGATATCATGTATAGGTTCTTTTACAAATCCTACATAATTTATATATATATAGC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.40%	3.70%	3.81%	0.00%	NA
All Indica	2759	88.70%	6.30%	4.93%	0.00%	NA
All Japonica	1512	99.90%	0.00%	0.13%	0.00%	NA
Aus	269	85.50%	0.00%	14.50%	0.00%	NA
Indica I	595	88.60%	3.40%	8.07%	0.00%	NA
Indica II	465	68.60%	23.20%	8.17%	0.00%	NA
Indica III	913	97.80%	0.20%	1.97%	0.00%	NA
Indica Intermediate	786	90.20%	5.70%	4.07%	0.00%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	2.20%	3.33%	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
vg0419549428	T -> G	LOC_Os04g32500-LOC_Os04g32510	intergenic_region ; MODIFIER	silent_mutation	Average:61.932; most accessible tissue: Minghui63 root, score: 75.485	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0419549428	7.08E-06	NA	mr1864_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