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Detailed information for vg0716392399:

Variant ID: vg0716392399 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 16392399
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 63. )

Flanking Sequence (100 bp) in Reference Genome:

CATTTTATGGAGTTGACAGTCAGTACTCACCCTCTCCCCCCGCGTTGTCCACGCGCGGGCGACATGGGAAAATCCCTAGCCGCCCCGTTTTTCTGATGGA[G/T]
CACACCGCCGGAAATCGGGCAACATGCTAGAATGGCAGGGGTGGGGTCATAACCCGACGATGCTTAGTCTCTAGTGCGGGGCAGAATGAGTTAAGCTAAA

Reverse complement sequence

TTTAGCTTAACTCATTCTGCCCCGCACTAGAGACTAAGCATCGTCGGGTTATGACCCCACCCCTGCCATTCTAGCATGTTGCCCGATTTCCGGCGGTGTG[C/A]
TCCATCAGAAAAACGGGGCGGCTAGGGATTTTCCCATGTCGCCCGCGCGTGGACAACGCGGGGGGAGAGGGTGAGTACTGACTGTCAACTCCATAAAATG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	90.20%	8.50%	0.19%	1.14%	NA
All Indica	2759	98.20%	0.70%	0.14%	0.98%	NA
All Japonica	1512	74.20%	23.70%	0.33%	1.79%	NA
Aus	269	94.40%	5.60%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.40%	0.40%	0.22%	0.00%	NA
Indica III	913	99.80%	0.10%	0.00%	0.11%	NA
Indica Intermediate	786	94.40%	1.90%	0.38%	3.31%	NA
Temperate Japonica	767	92.80%	3.70%	0.00%	3.52%	NA
Tropical Japonica	504	40.50%	58.70%	0.79%	0.00%	NA
Japonica Intermediate	241	85.50%	14.10%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	10.00%	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
vg0716392399	G -> DEL	N	N	silent_mutation	Average:69.913; most accessible tissue: Zhenshan97 young leaf, score: 88.127	N	N	N	N
vg0716392399	G -> T	LOC_Os07g28110.1	upstream_gene_variant ; 3786.0bp to feature; MODIFIER	silent_mutation	Average:69.913; most accessible tissue: Zhenshan97 young leaf, score: 88.127	N	N	N	N
vg0716392399	G -> T	LOC_Os07g28090.1	downstream_gene_variant ; 4953.0bp to feature; MODIFIER	silent_mutation	Average:69.913; most accessible tissue: Zhenshan97 young leaf, score: 88.127	N	N	N	N
vg0716392399	G -> T	LOC_Os07g28100.1	downstream_gene_variant ; 2032.0bp to feature; MODIFIER	silent_mutation	Average:69.913; most accessible tissue: Zhenshan97 young leaf, score: 88.127	N	N	N	N
vg0716392399	G -> T	LOC_Os07g28090-LOC_Os07g28100	intergenic_region ; MODIFIER	silent_mutation	Average:69.913; most accessible tissue: Zhenshan97 young leaf, score: 88.127	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0716392399	NA	2.37E-07	mr1229	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
vg0716392399	NA	1.22E-09	mr1449_2	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
vg0716392399	NA	8.03E-10	mr1705_2	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
vg0716392399	NA	8.01E-07	mr1705_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