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Detailed information for vg1205372323:

Variant ID: vg1205372323 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 5372323
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATGACGGCGGCCGGCAGTCAAGACAATGTCGCCATCAGCAACGGCGGCGGAGTTCATCAACCGTGGAGGTGAAGGCACCAATCAATGGCGGCGGATGCCA[C/T]
GTATGTATGTGCACACAAAAATAACAGATCAGAAAATAATTAGAAATCTGTGAATTAGATGACTAGAAAAATCAATATTAATTCTAGATTATGTAAGAAA

Reverse complement sequence

TTTCTTACATAATCTAGAATTAATATTGATTTTTCTAGTCATCTAATTCACAGATTTCTAATTATTTTCTGATCTGTTATTTTTGTGTGCACATACATAC[G/A]
TGGCATCCGCCGCCATTGATTGGTGCCTTCACCTCCACGGTTGATGAACTCCGCCGCCGTTGCTGATGGCGACATTGTCTTGACTGCCGGCCGCCGTCAT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	39.10%	3.90%	4.17%	52.88%	NA
All Indica	2759	12.90%	0.80%	5.04%	81.30%	NA
All Japonica	1512	84.80%	8.00%	2.25%	4.96%	NA
Aus	269	34.60%	1.10%	6.32%	57.99%	NA
Indica I	595	8.40%	0.20%	6.89%	84.54%	NA
Indica II	465	16.30%	0.00%	4.52%	79.14%	NA
Indica III	913	14.10%	1.10%	3.07%	81.71%	NA
Indica Intermediate	786	12.80%	1.30%	6.23%	79.64%	NA
Temperate Japonica	767	87.50%	6.60%	2.48%	3.39%	NA
Tropical Japonica	504	83.70%	9.90%	1.39%	4.96%	NA
Japonica Intermediate	241	78.40%	8.30%	3.32%	9.96%	NA
VI/Aromatic	96	63.50%	32.30%	2.08%	2.08%	NA
Intermediate	90	60.00%	8.90%	5.56%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1205372323	C -> DEL	N	N	silent_mutation	Average:13.545; most accessible tissue: Callus, score: 53.817	N	N	N	N
vg1205372323	C -> T	LOC_Os12g10160.1	upstream_gene_variant ; 163.0bp to feature; MODIFIER	silent_mutation	Average:13.545; most accessible tissue: Callus, score: 53.817	N	N	N	N
vg1205372323	C -> T	LOC_Os12g10170.1	upstream_gene_variant ; 2795.0bp to feature; MODIFIER	silent_mutation	Average:13.545; most accessible tissue: Callus, score: 53.817	N	N	N	N
vg1205372323	C -> T	LOC_Os12g10150.1	downstream_gene_variant ; 2161.0bp to feature; MODIFIER	silent_mutation	Average:13.545; most accessible tissue: Callus, score: 53.817	N	N	N	N
vg1205372323	C -> T	LOC_Os12g10180.1	downstream_gene_variant ; 4543.0bp to feature; MODIFIER	silent_mutation	Average:13.545; most accessible tissue: Callus, score: 53.817	N	N	N	N
vg1205372323	C -> T	LOC_Os12g10160-LOC_Os12g10170	intergenic_region ; MODIFIER	silent_mutation	Average:13.545; most accessible tissue: Callus, score: 53.817	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1205372323	2.14E-06	NA	mr1024	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