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Detailed information for vg0122013494:

Variant ID: vg0122013494 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 22013494
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAGTGCACATCTGTACACACAGTGCCGACACTATATCCATACGTGCAACTGCATAACAGCCCTCCCTCCAGAACCCGGCACTATATCCATACGTGCAACT[G/A]
CATAACAGCCCTCCCTCCAGAACCGCGTAGCCAGCCCAGGGCTGGCTCACTTACGCATACCACCCCACTTACATTTTTATCCTCGTTTCATATAAAACGG

Reverse complement sequence

CCGTTTTATATGAAACGAGGATAAAAATGTAAGTGGGGTGGTATGCGTAAGTGAGCCAGCCCTGGGCTGGCTACGCGGTTCTGGAGGGAGGGCTGTTATG[C/T]
AGTTGCACGTATGGATATAGTGCCGGGTTCTGGAGGGAGGGCTGTTATGCAGTTGCACGTATGGATATAGTGTCGGCACTGTGTGTACAGATGTGCACTA

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	96.00%	1.70%	2.33%	0.00%	NA
All Indica	2759	99.90%	0.00%	0.07%	0.00%	NA
All Japonica	1512	87.80%	5.20%	6.94%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.00%	0.13%	0.00%	NA
Temperate Japonica	767	80.70%	7.30%	11.99%	0.00%	NA
Tropical Japonica	504	99.00%	0.40%	0.60%	0.00%	NA
Japonica Intermediate	241	87.10%	8.70%	4.15%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	0.00%	3.33%	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
vg0122013494	G -> A	LOC_Os01g39120-LOC_Os01g39134	intergenic_region ; MODIFIER	silent_mutation	Average:51.256; most accessible tissue: Zhenshan97 panicle, score: 69.946	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0122013494	1.52E-06	2.41E-06	mr1201	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
vg0122013494	3.20E-07	2.35E-06	mr1201_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