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Detailed information for vg0432639639:

Variant ID: vg0432639639 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 32639639
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGATTTAGATATTATTATCAAAAGATATGTCTTTTGTAATAATTCCTATATCAATGGGTAGATAACTAGGAAAACATGCTTACGACAAACAAGGAGCAAC[C/T]
AATCCGATAATTACTCTAGAACTTATTGCTTATTTACTAAAACGTTTAATATGTAGTATGTAATATACTTTATGAATAAAAAATATCCTAATATATCAAT

Reverse complement sequence

ATTGATATATTAGGATATTTTTTATTCATAAAGTATATTACATACTACATATTAAACGTTTTAGTAAATAAGCAATAAGTTCTAGAGTAATTATCGGATT[G/A]
GTTGCTCCTTGTTTGTCGTAAGCATGTTTTCCTAGTTATCTACCCATTGATATAGGAATTATTACAAAAGACATATCTTTTGATAATAATATCTAAATCC

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	97.90%	1.10%	0.95%	0.00%	NA
All Indica	2759	99.80%	0.00%	0.18%	0.00%	NA
All Japonica	1512	94.20%	3.30%	2.45%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.30%	0.00%	0.67%	0.00%	NA
Indica II	465	99.80%	0.00%	0.22%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	93.20%	2.00%	4.82%	0.00%	NA
Tropical Japonica	504	99.00%	1.00%	0.00%	0.00%	NA
Japonica Intermediate	241	87.60%	12.40%	0.00%	0.00%	NA
VI/Aromatic	96	92.70%	4.20%	3.12%	0.00%	NA
Intermediate	90	100.00%	0.00%	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
vg0432639639	C -> T	LOC_Os04g54870.1	upstream_gene_variant ; 1836.0bp to feature; MODIFIER	silent_mutation	Average:33.79; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg0432639639	C -> T	LOC_Os04g54880.1	upstream_gene_variant ; 3863.0bp to feature; MODIFIER	silent_mutation	Average:33.79; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg0432639639	C -> T	LOC_Os04g54870.2	upstream_gene_variant ; 1802.0bp to feature; MODIFIER	silent_mutation	Average:33.79; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg0432639639	C -> T	LOC_Os04g54860.1	downstream_gene_variant ; 4818.0bp to feature; MODIFIER	silent_mutation	Average:33.79; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg0432639639	C -> T	LOC_Os04g54870-LOC_Os04g54880	intergenic_region ; MODIFIER	silent_mutation	Average:33.79; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0432639639	3.40E-06	7.53E-06	mr1829_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