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Detailed information for vg0407666707:

Variant ID: vg0407666707 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 7666707
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATACATTTATAGTTTATAATGAGAAGTGCCTGGAATTAATGAAAGAATTTCGGCTGGTTACTTTGAAGCATGTATCTCGAGAACAAAATCTTGAAGCTAA[T/C]
GATTTGGCTCAAGGGGCGTCGGGGTATAAGCCGATGATCAAAGATGTTAAGGTTGAAATTGCGGCAATGTCAGCCGATGACTGGAGGTATGATGTGCATC

Reverse complement sequence

GATGCACATCATACCTCCAGTCATCGGCTGACATTGCCGCAATTTCAACCTTAACATCTTTGATCATCGGCTTATACCCCGACGCCCCTTGAGCCAAATC[A/G]
TTAGCTTCAAGATTTTGTTCTCGAGATACATGCTTCAAAGTAACCAGCCGAAATTCTTTCATTAATTCCAGGCACTTCTCATTATAAACTATAAATGTAT

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	51.50%	0.50%	1.42%	46.53%	NA
All Indica	2759	26.90%	0.90%	2.14%	70.06%	NA
All Japonica	1512	99.20%	0.00%	0.00%	0.79%	NA
Aus	269	23.40%	0.00%	1.49%	75.09%	NA
Indica I	595	53.90%	0.20%	0.50%	45.38%	NA
Indica II	465	24.10%	0.90%	4.52%	70.54%	NA
Indica III	913	6.60%	1.50%	1.53%	90.36%	NA
Indica Intermediate	786	31.80%	0.60%	2.67%	64.89%	NA
Temperate Japonica	767	99.70%	0.00%	0.00%	0.26%	NA
Tropical Japonica	504	99.00%	0.00%	0.00%	0.99%	NA
Japonica Intermediate	241	97.90%	0.00%	0.00%	2.07%	NA
VI/Aromatic	96	69.80%	0.00%	3.12%	27.08%	NA
Intermediate	90	70.00%	0.00%	1.11%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0407666707	T -> C	LOC_Os04g13740.1	synonymous_variant ; p.Asn635Asn; LOW	synonymous_codon	Average:6.514; most accessible tissue: Callus, score: 16.951	N	N	N	N
vg0407666707	T -> DEL	LOC_Os04g13740.1	N	frameshift_variant	Average:6.514; most accessible tissue: Callus, score: 16.951	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0407666707	7.17E-06	NA	mr1193_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