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Detailed information for vg0722999471:

Variant ID: vg0722999471 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 22999471
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGGTTGATGTGATGGAAAAGGACTGAAGTTTGGATCCAAATTTTGGATCTAAACACAGCCTAAGGCCCTGTTTAGATCCTCCAAAATGGCAAAAGTTTTA[C/T]
CATTTTATAGCACTTTTTGCCATTTTGAATTTAAACACTAGTAGCAAAAGTTGGCAATTTGGCATTTGGCATTTGCTAGTCCATAGTAGCAAATTGTGCC

Reverse complement sequence

GGCACAATTTGCTACTATGGACTAGCAAATGCCAAATGCCAAATTGCCAACTTTTGCTACTAGTGTTTAAATTCAAAATGGCAAAAAGTGCTATAAAATG[G/A]
TAAAACTTTTGCCATTTTGGAGGATCTAAACAGGGCCTTAGGCTGTGTTTAGATCCAAAATTTGGATCCAAACTTCAGTCCTTTTCCATCACATCAACCT

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	38.30%	1.40%	0.44%	59.84%	NA
All Indica	2759	11.60%	0.00%	0.65%	87.79%	NA
All Japonica	1512	89.00%	4.30%	0.07%	6.61%	NA
Aus	269	1.10%	0.00%	0.00%	98.88%	NA
Indica I	595	2.50%	0.00%	1.18%	96.30%	NA
Indica II	465	18.30%	0.00%	0.65%	81.08%	NA
Indica III	913	13.00%	0.00%	0.77%	86.20%	NA
Indica Intermediate	786	12.70%	0.00%	0.13%	87.15%	NA
Temperate Japonica	767	90.20%	8.20%	0.00%	1.56%	NA
Tropical Japonica	504	85.30%	0.00%	0.20%	14.48%	NA
Japonica Intermediate	241	92.90%	0.80%	0.00%	6.22%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	53.30%	1.10%	2.22%	43.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0722999471	C -> DEL	N	N	silent_mutation	Average:64.926; most accessible tissue: Minghui63 panicle, score: 93.936	N	N	N	N
vg0722999471	C -> T	LOC_Os07g38300.1	upstream_gene_variant ; 3909.0bp to feature; MODIFIER	silent_mutation	Average:64.926; most accessible tissue: Minghui63 panicle, score: 93.936	N	N	N	N
vg0722999471	C -> T	LOC_Os07g38300.2	upstream_gene_variant ; 3909.0bp to feature; MODIFIER	silent_mutation	Average:64.926; most accessible tissue: Minghui63 panicle, score: 93.936	N	N	N	N
vg0722999471	C -> T	LOC_Os07g38300.5	upstream_gene_variant ; 3909.0bp to feature; MODIFIER	silent_mutation	Average:64.926; most accessible tissue: Minghui63 panicle, score: 93.936	N	N	N	N
vg0722999471	C -> T	LOC_Os07g38290.1	intron_variant ; MODIFIER	silent_mutation	Average:64.926; most accessible tissue: Minghui63 panicle, score: 93.936	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0722999471	NA	8.88E-06	mr1792_2	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