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Detailed information for vg1214376440:

Variant ID: vg1214376440 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 14376440
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCGTCGCCCTAGTCTTCCGCTGTTTTTTGTTTGTCTTCATGTGTGCTGGTCCTTCGCCGCCCATGTAATAAATTAACTATTTACGCTTCCACTTGTTAAA[C/T]
TCTGTATTGTATCAACTTTTGGTGTACCTTGCCTCCTGGGACAAGGAATAATACACGCACGTAAGGAACGCCCGTTGGGTTATTTCTGGTCATGACACTA

Reverse complement sequence

TAGTGTCATGACCAGAAATAACCCAACGGGCGTTCCTTACGTGCGTGTATTATTCCTTGTCCCAGGAGGCAAGGTACACCAAAAGTTGATACAATACAGA[G/A]
TTTAACAAGTGGAAGCGTAAATAGTTAATTTATTACATGGGCGGCGAAGGACCAGCACACATGAAGACAAACAAAAAACAGCGGAAGACTAGGGCGACGA

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	50.20%	1.20%	20.36%	28.18%	NA
All Indica	2759	46.50%	0.30%	20.88%	32.33%	NA
All Japonica	1512	63.30%	2.70%	12.50%	21.49%	NA
Aus	269	27.10%	2.20%	50.56%	20.07%	NA
Indica I	595	37.80%	0.00%	17.82%	44.37%	NA
Indica II	465	54.00%	0.40%	13.55%	32.04%	NA
Indica III	913	49.00%	0.50%	26.73%	23.77%	NA
Indica Intermediate	786	45.70%	0.30%	20.74%	33.33%	NA
Temperate Japonica	767	86.20%	0.80%	2.22%	10.82%	NA
Tropical Japonica	504	33.70%	6.30%	27.78%	32.14%	NA
Japonica Intermediate	241	52.30%	1.20%	13.28%	33.20%	NA
VI/Aromatic	96	14.60%	1.00%	40.62%	43.75%	NA
Intermediate	90	53.30%	1.10%	24.44%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1214376440	C -> DEL	N	N	silent_mutation	Average:10.442; most accessible tissue: Callus, score: 24.698	N	N	N	N
vg1214376440	C -> T	LOC_Os12g25040.1	upstream_gene_variant ; 1941.0bp to feature; MODIFIER	silent_mutation	Average:10.442; most accessible tissue: Callus, score: 24.698	N	N	N	N
vg1214376440	C -> T	LOC_Os12g25050.1	downstream_gene_variant ; 2736.0bp to feature; MODIFIER	silent_mutation	Average:10.442; most accessible tissue: Callus, score: 24.698	N	N	N	N
vg1214376440	C -> T	LOC_Os12g25040-LOC_Os12g25050	intergenic_region ; MODIFIER	silent_mutation	Average:10.442; most accessible tissue: Callus, score: 24.698	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1214376440	4.05E-06	4.05E-06	mr1634	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