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Detailed information for vg0432443707:

Variant ID: vg0432443707 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 32443707
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACTCGATGGCGGCGCCGCCGACGGCGATACCTGCTTTGTCATGTCGACGTATTCTTATCAAGGCAACATCCAAAAACGATATTTTTTTTTCACTTTTAAA[C/T]
CTTTTTTATTTTAAAAATAAATTCATCAAAAATTTATTTTAAAGTTAAACATTTTGTCCATATCAACCTACCTGGCATGGCAAGACAACACTGACATATC

Reverse complement sequence

GATATGTCAGTGTTGTCTTGCCATGCCAGGTAGGTTGATATGGACAAAATGTTTAACTTTAAAATAAATTTTTGATGAATTTATTTTTAAAATAAAAAAG[G/A]
TTTAAAAGTGAAAAAAAAATATCGTTTTTGGATGTTGCCTTGATAAGAATACGTCGACATGACAAAGCAGGTATCGCCGTCGGCGGCGCCGCCATCGAGT

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	94.00%	5.90%	0.04%	0.00%	NA
All Indica	2759	99.40%	0.50%	0.04%	0.00%	NA
All Japonica	1512	83.30%	16.70%	0.07%	0.00%	NA
Aus	269	97.40%	2.60%	0.00%	0.00%	NA
Indica I	595	99.50%	0.30%	0.17%	0.00%	NA
Indica II	465	98.30%	1.70%	0.00%	0.00%	NA
Indica III	913	99.70%	0.30%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.30%	0.00%	0.00%	NA
Temperate Japonica	767	76.70%	23.20%	0.13%	0.00%	NA
Tropical Japonica	504	93.30%	6.70%	0.00%	0.00%	NA
Japonica Intermediate	241	83.40%	16.60%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	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
vg0432443707	C -> T	LOC_Os04g54540.1	upstream_gene_variant ; 4229.0bp to feature; MODIFIER	silent_mutation	Average:53.395; most accessible tissue: Callus, score: 79.272	N	N	N	N
vg0432443707	C -> T	LOC_Os04g54550.1	downstream_gene_variant ; 1691.0bp to feature; MODIFIER	silent_mutation	Average:53.395; most accessible tissue: Callus, score: 79.272	N	N	N	N
vg0432443707	C -> T	LOC_Os04g54560.1	downstream_gene_variant ; 4783.0bp to feature; MODIFIER	silent_mutation	Average:53.395; most accessible tissue: Callus, score: 79.272	N	N	N	N
vg0432443707	C -> T	LOC_Os04g54540-LOC_Os04g54550	intergenic_region ; MODIFIER	silent_mutation	Average:53.395; most accessible tissue: Callus, score: 79.272	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0432443707	2.13E-06	NA	mr1406_2	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