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Detailed information for vg0118432044:

Variant ID: vg0118432044 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 18432044
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.62, C: 0.38, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:

TCCCTTTTGTTTGAAGGATGCCTCCCCGCAAGCAAACCTCCCACAAGCCCAAGCGCCCGAGGGACCGCTCTCCCACTCCATCCTCTCATGATGATTCGGA[T/C]
AGTGATTGGTCCGGTGGAGAGGAGGCGGTTCCTCAGGTTGCGCGGGTGGCTCGGGGCGGCAACCTCCCTCCTCGGCGATCTACTCATGCTCTTGGTGGTG

Reverse complement sequence

CACCACCAAGAGCATGAGTAGATCGCCGAGGAGGGAGGTTGCCGCCCCGAGCCACCCGCGCAACCTGAGGAACCGCCTCCTCTCCACCGGACCAATCACT[A/G]
TCCGAATCATCATGAGAGGATGGAGTGGGAGAGCGGTCCCTCGGGCGCTTGGGCTTGTGGGAGGTTTGCTTGCGGGGAGGCATCCTTCAAACAAAAGGGA

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	41.90%	25.80%	2.09%	30.28%	NA
All Indica	2759	8.60%	41.90%	3.48%	46.03%	NA
All Japonica	1512	96.10%	0.20%	0.07%	3.64%	NA
Aus	269	53.20%	11.50%	0.74%	34.57%	NA
Indica I	595	1.20%	50.40%	1.51%	46.89%	NA
Indica II	465	16.10%	67.50%	9.68%	6.67%	NA
Indica III	913	9.90%	14.50%	1.97%	73.71%	NA
Indica Intermediate	786	8.30%	52.20%	3.05%	36.51%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	89.10%	0.40%	0.20%	10.32%	NA
Japonica Intermediate	241	98.30%	0.40%	0.00%	1.24%	NA
VI/Aromatic	96	97.90%	0.00%	0.00%	2.08%	NA
Intermediate	90	56.70%	31.10%	0.00%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0118432044	T -> DEL	LOC_Os01g33470.1	N	frameshift_variant	Average:46.673; most accessible tissue: Minghui63 flag leaf, score: 82.289	N	N	N	N
vg0118432044	T -> C	LOC_Os01g33470.1	synonymous_variant ; p.Asp28Asp; LOW	synonymous_codon	Average:46.673; most accessible tissue: Minghui63 flag leaf, score: 82.289	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0118432044	NA	5.48E-08	mr1559	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
vg0118432044	NA	5.37E-06	mr1447_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