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Detailed information for vg1223970352:

Variant ID: vg1223970352 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 23970352
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATATGACATTTATGCCCTCTCCCAAATCTATTTATTAATTGTGTTTTTGCCACTATTATGCAATGGATTTGATTTTTTTTTCTGGTGAATATGTTTAAAA[C/T]
TAAATGACAGATTTGGACATTACAATTTGGACAAAATTTGAATTTGAAGAAATTTTGGCAAAATTTCGGCAGCATTTTAACAGAAATTGAACAAAATTTC

Reverse complement sequence

GAAATTTTGTTCAATTTCTGTTAAAATGCTGCCGAAATTTTGCCAAAATTTCTTCAAATTCAAATTTTGTCCAAATTGTAATGTCCAAATCTGTCATTTA[G/A]
TTTTAAACATATTCACCAGAAAAAAAAATCAAATCCATTGCATAATAGTGGCAAAAACACAATTAATAAATAGATTTGGGAGAGGGCATAAATGTCATAT

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	54.60%	2.60%	32.12%	10.64%	NA
All Indica	2759	33.30%	4.00%	48.97%	13.74%	NA
All Japonica	1512	99.30%	0.00%	0.60%	0.07%	NA
Aus	269	4.10%	4.50%	50.56%	40.89%	NA
Indica I	595	43.00%	1.80%	28.07%	27.06%	NA
Indica II	465	48.00%	3.70%	38.92%	9.46%	NA
Indica III	913	25.10%	6.70%	64.62%	3.61%	NA
Indica Intermediate	786	26.70%	2.80%	52.54%	17.94%	NA
Temperate Japonica	767	99.30%	0.00%	0.52%	0.13%	NA
Tropical Japonica	504	99.20%	0.00%	0.79%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	90.60%	1.00%	4.17%	4.17%	NA
Intermediate	90	68.90%	1.10%	20.00%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1223970352	C -> DEL	N	N	silent_mutation	Average:20.833; most accessible tissue: Minghui63 root, score: 36.81	N	N	N	N
vg1223970352	C -> T	LOC_Os12g38970.1	downstream_gene_variant ; 2286.0bp to feature; MODIFIER	silent_mutation	Average:20.833; most accessible tissue: Minghui63 root, score: 36.81	N	N	N	N
vg1223970352	C -> T	LOC_Os12g38980.1	downstream_gene_variant ; 361.0bp to feature; MODIFIER	silent_mutation	Average:20.833; most accessible tissue: Minghui63 root, score: 36.81	N	N	N	N
vg1223970352	C -> T	LOC_Os12g38970-LOC_Os12g38980	intergenic_region ; MODIFIER	silent_mutation	Average:20.833; most accessible tissue: Minghui63 root, score: 36.81	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1223970352	3.38E-07	3.37E-07	mr1392	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
vg1223970352	NA	6.19E-06	mr1856	Ind_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