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Detailed information for vg1213186520:

Variant ID: vg1213186520 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 13186520
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTGCGAGATAAATCTTTTAAGCCTAATTGTGCCATTTTTTGACAATGTGGTACTACAGTAAACATTTGCTAATAATGGATTAATTAGGATTAATAAATTC[G/A]
TCTCGCAGTTTCCTAGCGGAATCTATAATTTGTTTTGTTATTAGACAACGTTTAATACTTCAAATGTGTGTCCATATATCCGATGTGACACCCCAAAACA

Reverse complement sequence

TGTTTTGGGGTGTCACATCGGATATATGGACACACATTTGAAGTATTAAACGTTGTCTAATAACAAAACAAATTATAGATTCCGCTAGGAAACTGCGAGA[C/T]
GAATTTATTAATCCTAATTAATCCATTATTAGCAAATGTTTACTGTAGTACCACATTGTCAAAAAATGGCACAATTAGGCTTAAAAGATTTATCTCGCAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	49.70%	5.10%	16.21%	29.03%	NA
All Indica	2759	45.50%	1.50%	20.59%	32.48%	NA
All Japonica	1512	58.10%	7.30%	8.20%	26.32%	NA
Aus	269	43.10%	26.00%	18.22%	12.64%	NA
Indica I	595	19.50%	0.00%	30.42%	50.08%	NA
Indica II	465	62.60%	0.20%	12.90%	24.30%	NA
Indica III	913	54.90%	2.60%	18.07%	24.42%	NA
Indica Intermediate	786	44.00%	2.00%	20.61%	33.33%	NA
Temperate Japonica	767	83.40%	0.50%	1.56%	14.47%	NA
Tropical Japonica	504	29.00%	20.60%	17.66%	32.74%	NA
Japonica Intermediate	241	38.60%	1.20%	9.54%	50.62%	NA
VI/Aromatic	96	55.20%	8.30%	15.62%	20.83%	NA
Intermediate	90	52.20%	10.00%	11.11%	26.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1213186520	G -> DEL	N	N	silent_mutation	Average:17.88; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N
vg1213186520	G -> A	LOC_Os12g23280-LOC_Os12g23300	intergenic_region ; MODIFIER	silent_mutation	Average:17.88; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1213186520	5.29E-07	NA	mr1016	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
vg1213186520	1.08E-06	NA	mr1017	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
vg1213186520	4.06E-06	NA	mr1019	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
vg1213186520	9.12E-09	NA	mr1055	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
vg1213186520	3.53E-06	NA	mr1390	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
vg1213186520	9.21E-06	NA	mr1490	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
vg1213186520	NA	2.29E-08	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
vg1213186520	1.49E-06	NA	mr1023_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
vg1213186520	1.54E-08	NA	mr1055_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
vg1213186520	1.13E-08	NA	mr1132_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
vg1213186520	1.79E-06	NA	mr1178_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
vg1213186520	1.04E-08	NA	mr1390_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
vg1213186520	1.01E-08	NA	mr1490_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
vg1213186520	NA	6.28E-08	mr1850_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