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Detailed information for vg0401678473:

Variant ID: vg0401678473 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 1678473
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACCTCCCATCATCGCCCTATCACCCGTCCAAGTTCAACATATTTCATCAACCATTATTTAGTGTAAGTGCTCAAGTTTTATGCCCAATAATGCAAGTTGT[T/C]
TATATACCACAATTAATAGCACTGTCCATCCCTATAGTTCTATTAGCACTAAGCATGGCTAAGCATTAATGAATAAGACATCCCAAGTAATTCCAACCAG

Reverse complement sequence

CTGGTTGGAATTACTTGGGATGTCTTATTCATTAATGCTTAGCCATGCTTAGTGCTAATAGAACTATAGGGATGGACAGTGCTATTAATTGTGGTATATA[A/G]
ACAACTTGCATTATTGGGCATAAAACTTGAGCACTTACACTAAATAATGGTTGATGAAATATGTTGAACTTGGACGGGTGATAGGGCGATGATGGGAGGT

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	74.10%	0.10%	3.07%	22.68%	NA
All Indica	2759	86.30%	0.10%	2.79%	10.84%	NA
All Japonica	1512	56.70%	0.10%	0.60%	42.66%	NA
Aus	269	49.10%	0.70%	20.45%	29.74%	NA
Indica I	595	90.90%	0.00%	2.86%	6.22%	NA
Indica II	465	88.20%	0.00%	1.51%	10.32%	NA
Indica III	913	83.60%	0.10%	2.63%	13.69%	NA
Indica Intermediate	786	84.90%	0.10%	3.69%	11.32%	NA
Temperate Japonica	767	85.00%	0.00%	0.26%	14.73%	NA
Tropical Japonica	504	25.00%	0.20%	1.19%	73.61%	NA
Japonica Intermediate	241	32.80%	0.00%	0.41%	66.80%	NA
VI/Aromatic	96	70.80%	0.00%	2.08%	27.08%	NA
Intermediate	90	73.30%	0.00%	2.22%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0401678473	T -> C	LOC_Os04g03760.1	upstream_gene_variant ; 1628.0bp to feature; MODIFIER	silent_mutation	Average:8.426; most accessible tissue: Callus, score: 37.685	N	N	N	N
vg0401678473	T -> C	LOC_Os04g03760-LOC_Os04g03780	intergenic_region ; MODIFIER	silent_mutation	Average:8.426; most accessible tissue: Callus, score: 37.685	N	N	N	N
vg0401678473	T -> DEL	N	N	silent_mutation	Average:8.426; most accessible tissue: Callus, score: 37.685	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0401678473	4.32E-06	NA	mr1559	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
vg0401678473	NA	7.52E-06	mr1559	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