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Detailed information for vg1222354382:

Variant ID: vg1222354382 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 22354382
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAAGTATCTGAGTAAATTGTTCAGTACTTTTTCTGTCCCAAAATAACTCTTGAATATCTAGAAGGGATTACATCCCCATCTAAGTTGGGTGTTTTTTTTT[G/T]
GATTGAGGGAGTAGTACCCTTAGATAAGTTACGTTCATTCAACTATCTCAGCAAGTTGCATATCAGAAGTAATAGTAATAAAGCAGACAGTAGTGGTATG

Reverse complement sequence

CATACCACTACTGTCTGCTTTATTACTATTACTTCTGATATGCAACTTGCTGAGATAGTTGAATGAACGTAACTTATCTAAGGGTACTACTCCCTCAATC[C/A]
AAAAAAAAACACCCAACTTAGATGGGGATGTAATCCCTTCTAGATATTCAAGAGTTATTTTGGGACAGAAAAAGTACTGAACAATTTACTCAGATACTTT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	63.50%	5.10%	0.93%	30.47%	NA
All Indica	2759	52.90%	2.50%	1.34%	43.28%	NA
All Japonica	1512	84.30%	0.10%	0.26%	15.41%	NA
Aus	269	36.10%	62.50%	1.12%	0.37%	NA
Indica I	595	42.90%	0.20%	1.68%	55.29%	NA
Indica II	465	46.00%	0.20%	0.86%	52.90%	NA
Indica III	913	64.00%	3.90%	1.20%	30.89%	NA
Indica Intermediate	786	51.80%	3.80%	1.53%	42.88%	NA
Temperate Japonica	767	86.60%	0.00%	0.26%	13.17%	NA
Tropical Japonica	504	78.60%	0.00%	0.20%	21.23%	NA
Japonica Intermediate	241	88.80%	0.40%	0.41%	10.37%	NA
VI/Aromatic	96	95.80%	3.10%	0.00%	1.04%	NA
Intermediate	90	86.70%	1.10%	0.00%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1222354382	G -> DEL	N	N	silent_mutation	Average:10.479; most accessible tissue: Callus, score: 49.307	N	N	N	N
vg1222354382	G -> T	LOC_Os12g36510.1	upstream_gene_variant ; 1068.0bp to feature; MODIFIER	silent_mutation	Average:10.479; most accessible tissue: Callus, score: 49.307	N	N	N	N
vg1222354382	G -> T	LOC_Os12g36520.1	downstream_gene_variant ; 4763.0bp to feature; MODIFIER	silent_mutation	Average:10.479; most accessible tissue: Callus, score: 49.307	N	N	N	N
vg1222354382	G -> T	LOC_Os12g36510-LOC_Os12g36520	intergenic_region ; MODIFIER	silent_mutation	Average:10.479; most accessible tissue: Callus, score: 49.307	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1222354382	NA	4.86E-06	mr1608_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1222354382	1.35E-07	NA	mr1622_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