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Detailed information for vg0105181705:

Variant ID: vg0105181705 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 5181705
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGAACGACAGGTACATCGAGACTATACACCAAAATCATCTTTTCTCAGAGTACCTTCATTAGCTGCATAGGACATATAGATTGTTCCTCCGCCCTACTTG[G/A]
ACGGAAGCCGACATAGAGGATGACCGCGACTCCGATGAGGGGCGGAATCCCTATGATGTCCGGACTAGAGTTGGATATCAAATGGAGCACGCCCCACTTA

Reverse complement sequence

TAAGTGGGGCGTGCTCCATTTGATATCCAACTCTAGTCCGGACATCATAGGGATTCCGCCCCTCATCGGAGTCGCGGTCATCCTCTATGTCGGCTTCCGT[C/T]
CAAGTAGGGCGGAGGAACAATCTATATGTCCTATGCAGCTAATGAAGGTACTCTGAGAAAAGATGATTTTGGTGTATAGTCTCGATGTACCTGTCGTTCC

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	24.70%	24.10%	50.49%	0.76%	NA
All Indica	2759	14.80%	20.70%	63.25%	1.27%	NA
All Japonica	1512	47.10%	25.20%	27.71%	0.00%	NA
Aus	269	4.10%	45.70%	49.81%	0.37%	NA
Indica I	595	4.70%	31.90%	57.98%	5.38%	NA
Indica II	465	17.40%	10.50%	71.83%	0.22%	NA
Indica III	913	20.50%	16.00%	63.42%	0.11%	NA
Indica Intermediate	786	14.20%	23.70%	61.96%	0.13%	NA
Temperate Japonica	767	57.00%	26.50%	16.56%	0.00%	NA
Tropical Japonica	504	39.90%	22.20%	37.90%	0.00%	NA
Japonica Intermediate	241	30.70%	27.40%	41.91%	0.00%	NA
VI/Aromatic	96	16.70%	37.50%	45.83%	0.00%	NA
Intermediate	90	21.10%	30.00%	48.89%	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
vg0105181705	G -> A	LOC_Os01g09960.1	intron_variant ; MODIFIER	silent_mutation	Average:13.394; most accessible tissue: Callus, score: 28.384	N	N	N	N
vg0105181705	G -> DEL	N	N	silent_mutation	Average:13.394; most accessible tissue: Callus, score: 28.384	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0105181705	3.50E-08	3.68E-08	mr1057_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