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Detailed information for vg1214823299:

Variant ID: vg1214823299 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 14823299
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCGAACCGGATAAGTCGTGCGTAACTAATCCGGACTCCATGCCGTTTTCACGCACCGGATTTTCCGGAATGTTTCCAACAACAAAACAAATCCGAATTTT[C/T]
CTGCAGCAAAACAAAACTGGAGTAGTCTACGAGCGACGGCGCAGCACAGAGGAGGAGGCAAACCCTAGATTGATTTCACGTGTGTTGCGTGAAGGCAGCG

Reverse complement sequence

CGCTGCCTTCACGCAACACACGTGAAATCAATCTAGGGTTTGCCTCCTCCTCTGTGCTGCGCCGTCGCTCGTAGACTACTCCAGTTTTGTTTTGCTGCAG[G/A]
AAAATTCGGATTTGTTTTGTTGTTGGAAACATTCCGGAAAATCCGGTGCGTGAAAACGGCATGGAGTCCGGATTAGTTACGCACGACTTATCCGGTTCGG

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	55.10%	8.70%	8.84%	27.38%	NA
All Indica	2759	31.60%	11.70%	13.16%	43.53%	NA
All Japonica	1512	87.00%	5.30%	3.24%	4.43%	NA
Aus	269	97.00%	0.40%	0.37%	2.23%	NA
Indica I	595	56.50%	4.00%	10.25%	29.24%	NA
Indica II	465	21.10%	22.40%	24.30%	32.26%	NA
Indica III	913	18.20%	10.60%	10.51%	60.68%	NA
Indica Intermediate	786	34.70%	12.30%	11.83%	41.09%	NA
Temperate Japonica	767	93.50%	1.70%	0.91%	3.91%	NA
Tropical Japonica	504	79.00%	9.30%	6.75%	4.96%	NA
Japonica Intermediate	241	83.40%	8.30%	3.32%	4.98%	NA
VI/Aromatic	96	91.70%	0.00%	1.04%	7.29%	NA
Intermediate	90	71.10%	10.00%	4.44%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1214823299	C -> DEL	N	N	silent_mutation	Average:49.174; most accessible tissue: Minghui63 panicle, score: 82.128	N	N	N	N
vg1214823299	C -> T	LOC_Os12g25600.1	upstream_gene_variant ; 3502.0bp to feature; MODIFIER	silent_mutation	Average:49.174; most accessible tissue: Minghui63 panicle, score: 82.128	N	N	N	N
vg1214823299	C -> T	LOC_Os12g25610.1	upstream_gene_variant ; 61.0bp to feature; MODIFIER	silent_mutation	Average:49.174; most accessible tissue: Minghui63 panicle, score: 82.128	N	N	N	N
vg1214823299	C -> T	LOC_Os12g25630.1	downstream_gene_variant ; 4013.0bp to feature; MODIFIER	silent_mutation	Average:49.174; most accessible tissue: Minghui63 panicle, score: 82.128	N	N	N	N
vg1214823299	C -> T	LOC_Os12g25610-LOC_Os12g25630	intergenic_region ; MODIFIER	silent_mutation	Average:49.174; most accessible tissue: Minghui63 panicle, score: 82.128	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1214823299	NA	1.76E-06	mr1579	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
vg1214823299	3.59E-06	NA	mr1726	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