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Detailed information for vg0400771041:

Variant ID: vg0400771041 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 771041
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCCCGTCCGAGTGGTTTGAAGCCAACTTAGATGAGATGATCTTGGAGTAGATCTCGGCCGAGTTCGGGAGACCGAACGGGGCGGAGACCTCGTCTCTTCC[T/C]
GACTGGTTTGAATCCAAGTCAGGGAGAGAGATCTTAACGAAGTTGTCGGTGATGAAGTCGAGGCCGCCGAACCGGAACGCCTGTTGGTATTTCTTACAAT

Reverse complement sequence

ATTGTAAGAAATACCAACAGGCGTTCCGGTTCGGCGGCCTCGACTTCATCACCGACAACTTCGTTAAGATCTCTCTCCCTGACTTGGATTCAAACCAGTC[A/G]
GGAAGAGACGAGGTCTCCGCCCCGTTCGGTCTCCCGAACTCGGCCGAGATCTACTCCAAGATCATCTCATCTAAGTTGGCTTCAAACCACTCGGACGGGA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	59.70%	5.10%	1.27%	33.98%	NA
All Indica	2759	34.00%	8.60%	1.99%	55.49%	NA
All Japonica	1512	96.60%	0.10%	0.00%	3.37%	NA
Aus	269	99.60%	0.00%	0.00%	0.37%	NA
Indica I	595	17.10%	2.00%	1.51%	79.33%	NA
Indica II	465	41.10%	1.50%	1.94%	55.48%	NA
Indica III	913	38.30%	19.50%	2.52%	39.65%	NA
Indica Intermediate	786	37.40%	5.00%	1.78%	55.85%	NA
Temperate Japonica	767	99.70%	0.00%	0.00%	0.26%	NA
Tropical Japonica	504	90.70%	0.00%	0.00%	9.33%	NA
Japonica Intermediate	241	98.80%	0.40%	0.00%	0.83%	NA
VI/Aromatic	96	93.80%	1.00%	3.12%	2.08%	NA
Intermediate	90	73.30%	1.10%	2.22%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0400771041	T -> C	LOC_Os04g02230.1	upstream_gene_variant ; 288.0bp to feature; MODIFIER	silent_mutation	Average:44.18; most accessible tissue: Minghui63 flag leaf, score: 78.472	N	N	N	N
vg0400771041	T -> C	LOC_Os04g02240.1	upstream_gene_variant ; 3738.0bp to feature; MODIFIER	silent_mutation	Average:44.18; most accessible tissue: Minghui63 flag leaf, score: 78.472	N	N	N	N
vg0400771041	T -> C	LOC_Os04g02230-LOC_Os04g02240	intergenic_region ; MODIFIER	silent_mutation	Average:44.18; most accessible tissue: Minghui63 flag leaf, score: 78.472	N	N	N	N
vg0400771041	T -> DEL	N	N	silent_mutation	Average:44.18; most accessible tissue: Minghui63 flag leaf, score: 78.472	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0400771041	NA	1.39E-06	mr1346	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
vg0400771041	NA	3.14E-06	mr1346	Ind_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
vg0400771041	NA	4.47E-06	mr1438	Ind_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
vg0400771041	7.28E-06	NA	mr1733	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
vg0400771041	3.49E-06	3.16E-06	mr1733	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
vg0400771041	3.57E-08	1.90E-07	mr1745	Ind_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