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Detailed information for vg0429946245:

Variant ID: vg0429946245 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 29946245
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.00, others allele: 0.00, population size: 300. )

Flanking Sequence (100 bp) in Reference Genome:

CTTGTATGTTTGCGGTAGCCTCCCACCAATCTAGCACCGTTGAAGTTTGCCGCCATTGGCTAGGATTTTGTTGCTCGCACGTCACCCACTCCGCTAGTGC[C/T]
GCCCAGACTCTCCTTGTGTATCTACATTCTGCTAGGAGGTGCATGGCTGTTTTCTGGGTCCGACGACATAAGGGGCAGATGGAACCGTTTGGCCAACCTC

Reverse complement sequence

GAGGTTGGCCAAACGGTTCCATCTGCCCCTTATGTCGTCGGACCCAGAAAACAGCCATGCACCTCCTAGCAGAATGTAGATACACAAGGAGAGTCTGGGC[G/A]
GCACTAGCGGAGTGGGTGACGTGCGAGCAACAAAATCCTAGCCAATGGCGGCAAACTTCAACGGTGCTAGATTGGTGGGAGGCTACCGCAAACATACAAG

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	89.40%	10.60%	0.02%	0.00%	NA
All Indica	2759	95.70%	4.30%	0.00%	0.00%	NA
All Japonica	1512	82.70%	17.30%	0.00%	0.00%	NA
Aus	269	90.30%	9.70%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	93.50%	6.50%	0.00%	0.00%	NA
Indica III	913	95.60%	4.40%	0.00%	0.00%	NA
Indica Intermediate	786	93.90%	6.10%	0.00%	0.00%	NA
Temperate Japonica	767	99.00%	1.00%	0.00%	0.00%	NA
Tropical Japonica	504	52.60%	47.40%	0.00%	0.00%	NA
Japonica Intermediate	241	94.20%	5.80%	0.00%	0.00%	NA
VI/Aromatic	96	17.70%	82.30%	0.00%	0.00%	NA
Intermediate	90	80.00%	18.90%	1.11%	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
vg0429946245	C -> T	LOC_Os04g50188.1	synonymous_variant ; p.Ala15Ala; LOW	synonymous_codon	Average:59.717; most accessible tissue: Minghui63 root, score: 73.351	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0429946245	NA	9.49E-07	mr1082	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
vg0429946245	NA	8.87E-06	mr1890	Jap_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