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Detailed information for vg0114145969:

Variant ID: vg0114145969 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 14145969
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TATGTCAGATAACTAGGATGTATGTATACTATGTATACTAGAAGTATATGAATAGATTCTCTTTCTATTTTTGTTTCCACTTAGCTTGGATATTTTAGTA[T/C]
GAGAATGAGTAGCTTCCTGCTTGTATGTCAATCTATCCTTGGATTAACTTAACCCCTGCTTAGACTATGATTATTACAAGTAACATGTAAATTATTAGTC

Reverse complement sequence

GACTAATAATTTACATGTTACTTGTAATAATCATAGTCTAAGCAGGGGTTAAGTTAATCCAAGGATAGATTGACATACAAGCAGGAAGCTACTCATTCTC[A/G]
TACTAAAATATCCAAGCTAAGTGGAAACAAAAATAGAAAGAGAATCTATTCATATACTTCTAGTATACATAGTATACATACATCCTAGTTATCTGACATA

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	86.20%	1.40%	1.33%	11.02%	NA
All Indica	2759	80.50%	0.00%	0.94%	18.48%	NA
All Japonica	1512	93.30%	4.40%	2.38%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.50%	0.00%	0.00%	0.50%	NA
Indica II	465	57.60%	0.20%	2.15%	40.00%	NA
Indica III	913	77.70%	0.00%	0.88%	21.47%	NA
Indica Intermediate	786	83.10%	0.00%	1.02%	15.90%	NA
Temperate Japonica	767	90.70%	5.20%	4.04%	0.00%	NA
Tropical Japonica	504	99.40%	0.20%	0.40%	0.00%	NA
Japonica Intermediate	241	88.40%	10.40%	1.24%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	86.70%	1.10%	1.11%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0114145969	T -> DEL	N	N	silent_mutation	Average:26.611; most accessible tissue: Zhenshan97 flag leaf, score: 58.772	N	N	N	N
vg0114145969	T -> C	LOC_Os01g25070.1	upstream_gene_variant ; 4020.0bp to feature; MODIFIER	silent_mutation	Average:26.611; most accessible tissue: Zhenshan97 flag leaf, score: 58.772	N	N	N	N
vg0114145969	T -> C	LOC_Os01g25065-LOC_Os01g25070	intergenic_region ; MODIFIER	silent_mutation	Average:26.611; most accessible tissue: Zhenshan97 flag leaf, score: 58.772	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0114145969	7.90E-08	7.90E-08	mr1935	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