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Detailed information for vg0112129025:

Variant ID: vg0112129025 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 12129025
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCTCGCACGGCCCCTCCACGCGCCCCCACCACGTGTGCCCGTTGCAATAGCCGCCCGAATATAATGGGAACGCCCTATTAAGGGGGGTATGTTTCATTTT[T/C]
TGTTCCACCAACAATGTTTCAACTAGTGTACTCATGATGTTTCTTTATGTATGGATCAAATGTTGCAATGGATTTTTGATACTGTTTAATAATTTCATCT

Reverse complement sequence

AGATGAAATTATTAAACAGTATCAAAAATCCATTGCAACATTTGATCCATACATAAAGAAACATCATGAGTACACTAGTTGAAACATTGTTGGTGGAACA[A/G]
AAAATGAAACATACCCCCCTTAATAGGGCGTTCCCATTATATTCGGGCGGCTATTGCAACGGGCACACGTGGTGGGGGCGCGTGGAGGGGCCGTGCGAGG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	96.90%	2.00%	1.14%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	90.70%	5.70%	3.57%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.10%	0.90%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	83.60%	10.20%	6.26%	0.00%	NA
Tropical Japonica	504	99.60%	0.20%	0.20%	0.00%	NA
Japonica Intermediate	241	95.00%	2.90%	2.07%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	0.00%	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
vg0112129025	T -> C	LOC_Os01g21640.1	downstream_gene_variant ; 1792.0bp to feature; MODIFIER	silent_mutation	Average:43.822; most accessible tissue: Zhenshan97 flag leaf, score: 64.225	N	N	N	N
vg0112129025	T -> C	LOC_Os01g21650.1	downstream_gene_variant ; 569.0bp to feature; MODIFIER	silent_mutation	Average:43.822; most accessible tissue: Zhenshan97 flag leaf, score: 64.225	N	N	N	N
vg0112129025	T -> C	LOC_Os01g21640-LOC_Os01g21650	intergenic_region ; MODIFIER	silent_mutation	Average:43.822; most accessible tissue: Zhenshan97 flag leaf, score: 64.225	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0112129025	4.44E-06	4.44E-06	mr1012	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