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Detailed information for vg0408292601:

Variant ID: vg0408292601 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 8292601
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: 127. )

Flanking Sequence (100 bp) in Reference Genome:

CCTCGGTTTCTCACCCTCAGAGCAATGGACAAGTCGAGAGGGCAAACGGCATAGTACTACAAGGAATCAAGACCCGCGTCTACGACAGGCTCATGTCACA[T/C]
GACAAGAAGTGGGTCGAGGAACTTCCATCAGTACTATGGGTCGTGCGTACCACACCGACAACGTCCAACAAGTAGACACCCTTCTTCCTTATGTACGGCT

Reverse complement sequence

AGCCGTACATAAGGAAGAAGGGTGTCTACTTGTTGGACGTTGTCGGTGTGGTACGCACGACCCATAGTACTGATGGAAGTTCCTCGACCCACTTCTTGTC[A/G]
TGTGACATGAGCCTGTCGTAGACGCGGGTCTTGATTCCTTGTAGTACTATGCCGTTTGCCCTCTCGACTTGTCCATTGCTCTGAGGGTGAGAAACCGAGG

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	62.60%	24.40%	5.71%	7.26%	NA
All Indica	2759	93.00%	4.60%	2.25%	0.11%	NA
All Japonica	1512	2.90%	65.50%	10.32%	21.23%	NA
Aus	269	94.40%	3.00%	2.60%	0.00%	NA
Indica I	595	96.50%	1.70%	1.85%	0.00%	NA
Indica II	465	93.50%	4.10%	1.94%	0.43%	NA
Indica III	913	90.30%	7.10%	2.63%	0.00%	NA
Indica Intermediate	786	93.30%	4.30%	2.29%	0.13%	NA
Temperate Japonica	767	0.50%	95.80%	1.04%	2.61%	NA
Tropical Japonica	504	6.30%	16.70%	23.21%	53.77%	NA
Japonica Intermediate	241	3.30%	71.40%	12.86%	12.45%	NA
VI/Aromatic	96	52.10%	2.10%	35.42%	10.42%	NA
Intermediate	90	51.10%	26.70%	12.22%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0408292601	T -> C	LOC_Os04g14770.1	synonymous_variant ; p.His1766His; LOW	synonymous_codon	Average:11.494; most accessible tissue: Callus, score: 22.565	N	N	N	N
vg0408292601	T -> DEL	LOC_Os04g14770.1	N	frameshift_variant	Average:11.494; most accessible tissue: Callus, score: 22.565	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0408292601	NA	6.95E-07	mr1690	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
vg0408292601	2.14E-06	NA	mr1410_2	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