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Detailed information for vg0431890043:

Variant ID: vg0431890043 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 31890043
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAGGTAGGTCCGCCAATCTGCCTTGCAGACGAGACAACAGATTAAGTGCGATCCTAACAATGCATAATATTTTTCAAGCAACATAATTAAATTTCAAATA[C/T]
AGGCTCAAGATGTTCAAAGGTGGCTTGCCTTGCTCGAGATCTGGAGCTTGATCCTCGAAATCCTCGCACTGCGGGTCTTCGGGCTCCGAAACTACACGCG

Reverse complement sequence

CGCGTGTAGTTTCGGAGCCCGAAGACCCGCAGTGCGAGGATTTCGAGGATCAAGCTCCAGATCTCGAGCAAGGCAAGCCACCTTTGAACATCTTGAGCCT[G/A]
TATTTGAAATTTAATTATGTTGCTTGAAAAATATTATGCATTGTTAGGATCGCACTTAATCTGTTGTCTCGTCTGCAAGGCAGATTGGCGGACCTACCTA

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	33.40%	0.40%	12.61%	53.55%	NA
All Indica	2759	23.10%	0.60%	18.12%	58.21%	NA
All Japonica	1512	58.10%	0.10%	2.71%	39.15%	NA
Aus	269	11.90%	0.40%	15.99%	71.75%	NA
Indica I	595	22.20%	0.30%	12.10%	65.38%	NA
Indica II	465	25.40%	0.20%	12.26%	62.15%	NA
Indica III	913	26.60%	1.30%	24.53%	47.54%	NA
Indica Intermediate	786	18.20%	0.30%	18.70%	62.85%	NA
Temperate Japonica	767	86.70%	0.10%	0.65%	12.52%	NA
Tropical Japonica	504	23.80%	0.00%	5.16%	71.03%	NA
Japonica Intermediate	241	38.60%	0.00%	4.15%	57.26%	NA
VI/Aromatic	96	3.10%	0.00%	2.08%	94.79%	NA
Intermediate	90	34.40%	0.00%	11.11%	54.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0431890043	C -> DEL	N	N	silent_mutation	Average:11.757; most accessible tissue: Callus, score: 17.996	N	N	N	N
vg0431890043	C -> T	LOC_Os04g53520.1	intron_variant ; MODIFIER	silent_mutation	Average:11.757; most accessible tissue: Callus, score: 17.996	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0431890043	NA	3.44E-06	mr1782_2	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