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Detailed information for vg0704923207:

Variant ID: vg0704923207 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 4923207
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.06, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

ACCCGATATGAGTGCTATTATGCAACTCTGCCATGGACTTTGGTCCGGATCCGGATTCTCATTAGAGAAATATTAGCAATCATAGAGGCGATGTTGTCGA[C/T]
AACTATTCTTTTCTCCACATACTCATTCCGTGAGGTTAATTCATTATAAACCATATCTTAGTCATTTCCCAAACATAAGATGTATGATTGTTCCACATCC

Reverse complement sequence

GGATGTGGAACAATCATACATCTTATGTTTGGGAAATGACTAAGATATGGTTTATAATGAATTAACCTCACGGAATGAGTATGTGGAGAAAAGAATAGTT[G/A]
TCGACAACATCGCCTCTATGATTGCTAATATTTCTCTAATGAGAATCCGGATCCGGACCAAAGTCCATGGCAGAGTTGCATAATAGCACTCATATCGGGT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.80%	4.30%	2.90%	0.00%	NA
All Indica	2759	89.30%	6.90%	3.81%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	85.50%	3.70%	10.78%	0.00%	NA
Indica I	595	91.80%	2.50%	5.71%	0.00%	NA
Indica II	465	95.50%	3.20%	1.29%	0.00%	NA
Indica III	913	82.60%	13.40%	4.05%	0.00%	NA
Indica Intermediate	786	91.60%	4.80%	3.56%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	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
vg0704923207	C -> T	LOC_Os07g09340.1	downstream_gene_variant ; 2419.0bp to feature; MODIFIER	silent_mutation	Average:25.828; most accessible tissue: Minghui63 root, score: 43.505	N	N	N	N
vg0704923207	C -> T	LOC_Os07g09350.1	downstream_gene_variant ; 4548.0bp to feature; MODIFIER	silent_mutation	Average:25.828; most accessible tissue: Minghui63 root, score: 43.505	N	N	N	N
vg0704923207	C -> T	LOC_Os07g09340-LOC_Os07g09350	intergenic_region ; MODIFIER	silent_mutation	Average:25.828; most accessible tissue: Minghui63 root, score: 43.505	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0704923207	5.32E-06	7.79E-07	mr1789_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