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Detailed information for vg0123426824:

Variant ID: vg0123426824 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 23426824
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GATTCGTACTTCTGGTTGGAAAACCGGGACCATAGGGGGGTTACGAACCGGGATTAAAAAGCACTTCTCCGCCAGTGATAGCTCATGTTTTCACTTTGGG[C/A]
TAGAGTTTCTTTCCTTCTCAGATCACCACCCGACTGGGCACTGCCTGCACATCCTACCATCGCCGGCACCGTGAACCCTCTGCTGCTGCTGCCGCCGGCT

Reverse complement sequence

AGCCGGCGGCAGCAGCAGCAGAGGGTTCACGGTGCCGGCGATGGTAGGATGTGCAGGCAGTGCCCAGTCGGGTGGTGATCTGAGAAGGAAAGAAACTCTA[G/T]
CCCAAAGTGAAAACATGAGCTATCACTGGCGGAGAAGTGCTTTTTAATCCCGGTTCGTAACCCCCCTATGGTCCCGGTTTTCCAACCAGAAGTACGAATC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	78.10%	5.60%	1.69%	14.58%	NA
All Indica	2759	98.40%	0.00%	0.40%	1.20%	NA
All Japonica	1512	46.20%	17.30%	1.65%	34.79%	NA
Aus	269	52.80%	0.00%	14.87%	32.34%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	98.90%	0.00%	0.00%	1.08%	NA
Indica III	913	98.70%	0.00%	0.66%	0.66%	NA
Indica Intermediate	786	96.60%	0.10%	0.51%	2.80%	NA
Temperate Japonica	767	39.10%	26.90%	1.17%	32.86%	NA
Tropical Japonica	504	48.60%	1.00%	1.98%	48.41%	NA
Japonica Intermediate	241	63.90%	21.20%	2.49%	12.45%	NA
VI/Aromatic	96	71.90%	0.00%	1.04%	27.08%	NA
Intermediate	90	75.60%	2.20%	3.33%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0123426824	C -> A	LOC_Os01g41390.1	downstream_gene_variant ; 2455.0bp to feature; MODIFIER	silent_mutation	Average:68.978; most accessible tissue: Minghui63 root, score: 77.29	N	N	N	N
vg0123426824	C -> A	LOC_Os01g41390-LOC_Os01g41400	intergenic_region ; MODIFIER	silent_mutation	Average:68.978; most accessible tissue: Minghui63 root, score: 77.29	N	N	N	N
vg0123426824	C -> DEL	N	N	silent_mutation	Average:68.978; most accessible tissue: Minghui63 root, score: 77.29	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0123426824	NA	9.63E-06	mr1708	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
vg0123426824	9.02E-06	9.00E-06	mr1766_2	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
vg0123426824	2.65E-06	NA	mr1970_2	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