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Detailed information for vg0100948930:

Variant ID: vg0100948930 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 948930
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGTCCCATTGAATTAAACATTGATGCAAGGTAGAAGGCACACAACAATTTGCATGAATCCAACAACGACCCAAAATAACATTGTAGTTACCTTGCACATC[G/A]
ACGATGAAGAAAGCGGTTGGTAGCGTCTTATTTCCCACGGTGAGCTCCGCCGAAAAAATACCCCTCGCCTCCGTTGGTTCACCATTGAATCCATTGAGAA

Reverse complement sequence

TTCTCAATGGATTCAATGGTGAACCAACGGAGGCGAGGGGTATTTTTTCGGCGGAGCTCACCGTGGGAAATAAGACGCTACCAACCGCTTTCTTCATCGT[C/T]
GATGTGCAAGGTAACTACAATGTTATTTTGGGTCGTTGTTGGATTCATGCAAATTGTTGTGTGCCTTCTACCTTGCATCAATGTTTAATTCAATGGGACG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	87.00%	6.90%	6.03%	0.00%	NA
All Indica	2759	78.60%	11.70%	9.71%	0.00%	NA
All Japonica	1512	99.10%	0.10%	0.79%	0.00%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	90.60%	2.50%	6.89%	0.00%	NA
Indica II	465	72.90%	12.50%	14.62%	0.00%	NA
Indica III	913	72.50%	18.30%	9.20%	0.00%	NA
Indica Intermediate	786	79.90%	10.60%	9.54%	0.00%	NA
Temperate Japonica	767	98.80%	0.10%	1.04%	0.00%	NA
Tropical Japonica	504	99.20%	0.00%	0.79%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	4.40%	4.44%	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
vg0100948930	G -> A	LOC_Os01g02740.1	synonymous_variant ; p.Val833Val; LOW	synonymous_codon	Average:15.586; most accessible tissue: Minghui63 young leaf, score: 27.355	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0100948930	2.96E-06	NA	mr1738	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