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Detailed information for vg0403844302:

Variant ID: vg0403844302 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 3844302
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 322. )

Flanking Sequence (100 bp) in Reference Genome:

GTGTGAAGTTTCTTAGGGGTGACGGTTAGTATTTAAAGCGCTGCGGTAACGGTCGGAAAAACAGCAACGAGCGATATTCTTGGAGAAGCAGATATGGCAA[A/T]
TCCGAAACATTACCAAATATTCCGGACTTGGGGGGCATGTGTTAACAACCAAATTTGGTAATTTCAGTATCAGAGACAAAGATAAAACTGAGGTGGAATC

Reverse complement sequence

GATTCCACCTCAGTTTTATCTTTGTCTCTGATACTGAAATTACCAAATTTGGTTGTTAACACATGCCCCCCAAGTCCGGAATATTTGGTAATGTTTCGGA[T/A]
TTGCCATATCTGCTTCTCCAAGAATATCGCTCGTTGCTGTTTTTCCGACCGTTACCGCAGCGCTTTAAATACTAACCGTCACCCCTAAGAAACTTCACAC

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	93.40%	0.10%	0.44%	6.09%	NA
All Indica	2759	99.70%	0.00%	0.07%	0.18%	NA
All Japonica	1512	80.80%	0.20%	1.12%	17.92%	NA
Aus	269	95.90%	0.00%	0.74%	3.35%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.00%	0.00%	0.22%	NA
Indica III	913	99.80%	0.00%	0.00%	0.22%	NA
Indica Intermediate	786	99.50%	0.00%	0.25%	0.25%	NA
Temperate Japonica	767	97.00%	0.00%	0.13%	2.87%	NA
Tropical Japonica	504	62.90%	0.40%	2.58%	34.13%	NA
Japonica Intermediate	241	66.40%	0.40%	1.24%	31.95%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	0.00%	0.00%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0403844302	A -> DEL	N	N	silent_mutation	Average:43.762; most accessible tissue: Minghui63 young leaf, score: 68.745	N	N	N	N
vg0403844302	A -> T	LOC_Os04g07240.1	upstream_gene_variant ; 219.0bp to feature; MODIFIER	silent_mutation	Average:43.762; most accessible tissue: Minghui63 young leaf, score: 68.745	N	N	N	N
vg0403844302	A -> T	LOC_Os04g07250.1	upstream_gene_variant ; 3303.0bp to feature; MODIFIER	silent_mutation	Average:43.762; most accessible tissue: Minghui63 young leaf, score: 68.745	N	N	N	N
vg0403844302	A -> T	LOC_Os04g07240-LOC_Os04g07250	intergenic_region ; MODIFIER	silent_mutation	Average:43.762; most accessible tissue: Minghui63 young leaf, score: 68.745	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0403844302	1.02E-06	NA	mr1794	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