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Detailed information for vg1213526586:

Variant ID: vg1213526586 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 13526586
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGGTTACTTTCTTGCAGTAACAATATTATAACGTTGTCAAAATATAGTGATGACGGATTTAGTTTTGTAAAGCTCTTTTTTTAAAGCATTATGGTGGAAA[C/T]
GGTTCAAAAATATAATATGTGATGCGAGAGATACGATTGTTTAAAGATTAGAATTTCAAATAATCCACTTGCGTTTAGTTTGCTATTATGTATCTTTTGT

Reverse complement sequence

ACAAAAGATACATAATAGCAAACTAAACGCAAGTGGATTATTTGAAATTCTAATCTTTAAACAATCGTATCTCTCGCATCACATATTATATTTTTGAACC[G/A]
TTTCCACCATAATGCTTTAAAAAAAGAGCTTTACAAAACTAAATCCGTCATCACTATATTTTGACAACGTTATAATATTGTTACTGCAAGAAAGTAACCC

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	79.80%	2.00%	2.37%	15.85%	NA
All Indica	2759	82.70%	0.10%	0.83%	16.42%	NA
All Japonica	1512	74.10%	6.00%	5.62%	14.29%	NA
Aus	269	87.40%	0.00%	0.74%	11.90%	NA
Indica I	595	76.60%	0.00%	1.01%	22.35%	NA
Indica II	465	83.40%	0.20%	1.72%	14.62%	NA
Indica III	913	86.10%	0.00%	0.55%	13.36%	NA
Indica Intermediate	786	82.80%	0.10%	0.51%	16.54%	NA
Temperate Japonica	767	86.80%	0.00%	1.69%	11.47%	NA
Tropical Japonica	504	53.60%	17.50%	12.50%	16.47%	NA
Japonica Intermediate	241	76.30%	1.20%	3.73%	18.67%	NA
VI/Aromatic	96	66.70%	0.00%	2.08%	31.25%	NA
Intermediate	90	78.90%	1.10%	0.00%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1213526586	C -> DEL	N	N	silent_mutation	Average:14.173; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N
vg1213526586	C -> T	LOC_Os12g23800.1	downstream_gene_variant ; 1246.0bp to feature; MODIFIER	silent_mutation	Average:14.173; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N
vg1213526586	C -> T	LOC_Os12g23790-LOC_Os12g23800	intergenic_region ; MODIFIER	silent_mutation	Average:14.173; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1213526586	NA	3.21E-06	mr1583	Jap_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
vg1213526586	7.48E-07	NA	mr1040_2	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
vg1213526586	NA	4.27E-06	mr1072_2	Jap_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
vg1213526586	NA	3.72E-06	mr1077_2	Jap_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
vg1213526586	NA	7.48E-08	mr1243_2	Jap_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
vg1213526586	NA	2.26E-08	mr1248_2	Jap_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
vg1213526586	NA	3.13E-07	mr1253_2	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
vg1213526586	NA	3.99E-06	mr1359_2	Jap_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
vg1213526586	7.02E-06	9.75E-10	mr1800_2	Jap_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