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Detailed information for vg0114635543:

Variant ID: vg0114635543 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 14635543
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

TTGTCTAATTGCGCTCAGGCACCGTCCTGTCCAAGTCGTCTAGGCCGCCTAGAACCGACTAGGACGGTAGGACCATCTAGGCGGTAAATCGACTAATTCA[C/T]
TGCCTAGGGTGTAAACTGGACAAATTGTCGCCGACTAGCGATTAATCACCATCTAGACGGGCTAGGCGGCCGTTTAGGCGAACATTGTTCTAAATGGATA

Reverse complement sequence

TATCCATTTAGAACAATGTTCGCCTAAACGGCCGCCTAGCCCGTCTAGATGGTGATTAATCGCTAGTCGGCGACAATTTGTCCAGTTTACACCCTAGGCA[G/A]
TGAATTAGTCGATTTACCGCCTAGATGGTCCTACCGTCCTAGTCGGTTCTAGGCGGCCTAGACGACTTGGACAGGACGGTGCCTGAGCGCAATTAGACAA

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	91.30%	6.00%	2.20%	0.44%	NA
All Indica	2759	96.00%	0.80%	2.50%	0.76%	NA
All Japonica	1512	82.70%	15.50%	1.85%	0.00%	NA
Aus	269	99.30%	0.00%	0.74%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	85.40%	1.50%	9.03%	4.09%	NA
Indica III	913	99.60%	0.30%	0.11%	0.00%	NA
Indica Intermediate	786	95.00%	1.40%	3.31%	0.25%	NA
Temperate Japonica	767	85.50%	11.70%	2.74%	0.00%	NA
Tropical Japonica	504	75.80%	23.40%	0.79%	0.00%	NA
Japonica Intermediate	241	88.00%	10.80%	1.24%	0.00%	NA
VI/Aromatic	96	83.30%	14.60%	2.08%	0.00%	NA
Intermediate	90	80.00%	16.70%	3.33%	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
vg0114635543	C -> T	LOC_Os01g25820-LOC_Os01g25839	intergenic_region ; MODIFIER	silent_mutation	Average:59.764; most accessible tissue: Minghui63 flag leaf, score: 75.722	N	N	N	N
vg0114635543	C -> DEL	N	N	silent_mutation	Average:59.764; most accessible tissue: Minghui63 flag leaf, score: 75.722	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0114635543	1.54E-06	NA	mr1601	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