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Detailed information for vg1200344922:

Variant ID: vg1200344922 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 344922
Reference Allele: A	Alternative Allele: T
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGGCTGCGCGTATATAGTTAGCTAGCCAGGTGGTAAATGGATTAAGGAGATGAGGGAGACATGCATGTTTGTGTCGTTTATATTGAGAAAGAGAGAAATA[A/T]
ATATAGGGGGGCTACGACAGCGGGGCGGCGCTGGATGGATGCTGTATATATATATGTGGCCGGGCAAGAGCGAGCACAGCCGGCCGGAGGAGGAATTAAG

Reverse complement sequence

CTTAATTCCTCCTCCGGCCGGCTGTGCTCGCTCTTGCCCGGCCACATATATATATACAGCATCCATCCAGCGCCGCCCCGCTGTCGTAGCCCCCCTATAT[T/A]
TATTTCTCTCTTTCTCAATATAAACGACACAAACATGCATGTCTCCCTCATCTCCTTAATCCATTTACCACCTGGCTAGCTAACTATATACGCGCAGCCA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	71.50%	22.20%	4.55%	1.80%	NA
All Indica	2759	94.20%	1.60%	1.45%	2.75%	NA
All Japonica	1512	31.90%	57.90%	9.79%	0.46%	NA
Aus	269	80.30%	12.30%	7.43%	0.00%	NA
Indica I	595	97.50%	0.70%	1.34%	0.50%	NA
Indica II	465	86.70%	2.40%	3.87%	7.10%	NA
Indica III	913	96.70%	0.90%	0.33%	2.08%	NA
Indica Intermediate	786	93.40%	2.50%	1.40%	2.67%	NA
Temperate Japonica	767	14.60%	73.70%	10.82%	0.91%	NA
Tropical Japonica	504	65.90%	26.20%	7.94%	0.00%	NA
Japonica Intermediate	241	15.80%	73.90%	10.37%	0.00%	NA
VI/Aromatic	96	32.30%	66.70%	1.04%	0.00%	NA
Intermediate	90	53.30%	37.80%	6.67%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1200344922	A -> DEL	N	N	silent_mutation	Average:39.321; most accessible tissue: Zhenshan97 flag leaf, score: 77.203	N	N	N	N
vg1200344922	A -> T	LOC_Os12g01570.1	upstream_gene_variant ; 162.0bp to feature; MODIFIER	silent_mutation	Average:39.321; most accessible tissue: Zhenshan97 flag leaf, score: 77.203	N	N	N	N
vg1200344922	A -> T	LOC_Os12g01560.1	downstream_gene_variant ; 3454.0bp to feature; MODIFIER	silent_mutation	Average:39.321; most accessible tissue: Zhenshan97 flag leaf, score: 77.203	N	N	N	N
vg1200344922	A -> T	LOC_Os12g01574.1	downstream_gene_variant ; 1401.0bp to feature; MODIFIER	silent_mutation	Average:39.321; most accessible tissue: Zhenshan97 flag leaf, score: 77.203	N	N	N	N
vg1200344922	A -> T	LOC_Os12g01560-LOC_Os12g01570	intergenic_region ; MODIFIER	silent_mutation	Average:39.321; most accessible tissue: Zhenshan97 flag leaf, score: 77.203	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1200344922	NA	3.20E-08	mr1425_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
vg1200344922	2.77E-06	NA	mr1748_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