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Detailed information for vg0402902417:

Variant ID: vg0402902417 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 2902417
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 43. )

Flanking Sequence (100 bp) in Reference Genome:

CTTGGATGAGTGGAGTAGCGACATTAGCGACTTCATCTCTTGCTCCTTCAAGCTTCTTGATCTTACCAACCAGGACGTCGAACTGAGCTTGCGATTTGAT[T/C]
TTGCGGTCTACAGAACACATTTATGATAAGAATCTGCTGCATTAAAAAGAGAGAAGTTCAGATTGTCAGCTGGCAGTACCTTCAACCTCCTTCAAGGCCG

Reverse complement sequence

CGGCCTTGAAGGAGGTTGAAGGTACTGCCAGCTGACAATCTGAACTTCTCTCTTTTTAATGCAGCAGATTCTTATCATAAATGTGTTCTGTAGACCGCAA[A/G]
ATCAAATCGCAAGCTCAGTTCGACGTCCTGGTTGGTAAGATCAAGAAGCTTGAAGGAGCAAGAGATGAAGTCGCTAATGTCGCTACTCCACTCATCCAAG

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	55.90%	25.30%	17.46%	1.38%	NA
All Indica	2759	74.00%	13.00%	12.79%	0.11%	NA
All Japonica	1512	25.70%	45.70%	24.47%	4.10%	NA
Aus	269	30.90%	43.10%	26.02%	0.00%	NA
Indica I	595	77.50%	13.10%	9.08%	0.34%	NA
Indica II	465	68.60%	19.60%	11.83%	0.00%	NA
Indica III	913	79.00%	6.10%	14.90%	0.00%	NA
Indica Intermediate	786	69.00%	17.20%	13.74%	0.13%	NA
Temperate Japonica	767	3.80%	76.00%	12.91%	7.30%	NA
Tropical Japonica	504	53.00%	12.10%	34.72%	0.20%	NA
Japonica Intermediate	241	38.60%	19.50%	39.83%	2.07%	NA
VI/Aromatic	96	76.00%	6.20%	17.71%	0.00%	NA
Intermediate	90	58.90%	24.40%	16.67%	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
vg0402902417	T -> C	LOC_Os04g05680.1	synonymous_variant ; p.Lys659Lys; LOW	synonymous_codon	Average:31.883; most accessible tissue: Minghui63 young leaf, score: 61.007	N	N	N	N
vg0402902417	T -> DEL	LOC_Os04g05680.1	N	frameshift_variant	Average:31.883; most accessible tissue: Minghui63 young leaf, score: 61.007	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0402902417	NA	9.43E-06	mr1159	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