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Detailed information for vg0709789120:

Variant ID: vg0709789120 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 9789120
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 43. )

Flanking Sequence (100 bp) in Reference Genome:

GTTAGGTGCGCACGGAGGTGAGGAAGCTCGGCCGCCCGTCCTCCTTCGCCGCCGACCACCGGAGCTCCGCCACCGCCTTCCTCCTCGTCGCCGGCCATCA[C/T]
CGTTCGTCGATAGACGTTGTGGTGAGTACCATCGGGTTCGTCTCGATGTTCACTACAACAAAACCATTGTTTTAAGACGTTTCACTTAAGTCATTCTATA

Reverse complement sequence

TATAGAATGACTTAAGTGAAACGTCTTAAAACAATGGTTTTGTTGTAGTGAACATCGAGACGAACCCGATGGTACTCACCACAACGTCTATCGACGAACG[G/A]
TGATGGCCGGCGACGAGGAGGAAGGCGGTGGCGGAGCTCCGGTGGTCGGCGGCGAAGGAGGACGGGCGGCCGAGCTTCCTCACCTCCGTGCGCACCTAAC

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	36.40%	1.50%	28.42%	33.66%	NA
All Indica	2759	12.10%	2.20%	44.47%	41.25%	NA
All Japonica	1512	76.50%	0.20%	2.25%	21.03%	NA
Aus	269	62.10%	0.70%	17.84%	19.33%	NA
Indica I	595	26.20%	2.00%	22.35%	49.41%	NA
Indica II	465	6.70%	0.40%	29.89%	63.01%	NA
Indica III	913	0.50%	4.30%	72.40%	22.78%	NA
Indica Intermediate	786	17.90%	1.00%	37.40%	43.64%	NA
Temperate Japonica	767	76.00%	0.30%	1.30%	22.43%	NA
Tropical Japonica	504	88.70%	0.20%	2.58%	8.53%	NA
Japonica Intermediate	241	52.70%	0.00%	4.56%	42.74%	NA
VI/Aromatic	96	28.10%	5.20%	16.67%	50.00%	NA
Intermediate	90	41.10%	0.00%	20.00%	38.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0709789120	C -> DEL	N	N	silent_mutation	Average:25.81; most accessible tissue: Minghui63 root, score: 52.955	N	N	N	N
vg0709789120	C -> T	LOC_Os07g16680.1	upstream_gene_variant ; 2454.0bp to feature; MODIFIER	silent_mutation	Average:25.81; most accessible tissue: Minghui63 root, score: 52.955	N	N	N	N
vg0709789120	C -> T	LOC_Os07g16690.1	upstream_gene_variant ; 1778.0bp to feature; MODIFIER	silent_mutation	Average:25.81; most accessible tissue: Minghui63 root, score: 52.955	N	N	N	N
vg0709789120	C -> T	LOC_Os07g16700.1	upstream_gene_variant ; 4184.0bp to feature; MODIFIER	silent_mutation	Average:25.81; most accessible tissue: Minghui63 root, score: 52.955	N	N	N	N
vg0709789120	C -> T	LOC_Os07g16670.1	downstream_gene_variant ; 3869.0bp to feature; MODIFIER	silent_mutation	Average:25.81; most accessible tissue: Minghui63 root, score: 52.955	N	N	N	N
vg0709789120	C -> T	LOC_Os07g16680-LOC_Os07g16690	intergenic_region ; MODIFIER	silent_mutation	Average:25.81; most accessible tissue: Minghui63 root, score: 52.955	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0709789120	4.13E-06	NA	mr1416	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