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Detailed information for vg1215354257:

Variant ID: vg1215354257 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 15354257
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACTCCTAAGCTCGCAAAATCTTTTCTCGTCTAAGGGCTTGGTGAAAATGTCGGCCAATTGGCTCTCGGTTTCTCACATGTGTAAGGCAAATGTCTCCTTT[G/A]
GTCTCATGATCTCTCAAAAAGTGATGGCGAATATCTATGTGTTTGGTTCGAGAATGTTGAACGGGATTATTGGCTATTTTGATGGCACTCTCATTGTCAC

Reverse complement sequence

GTGACAATGAGAGTGCCATCAAAATAGCCAATAATCCCGTTCAACATTCTCGAACCAAACACATAGATATTCGCCATCACTTTTTGAGAGATCATGAGAC[C/T]
AAAGGAGACATTTGCCTTACACATGTGAGAAACCGAGAGCCAATTGGCCGACATTTTCACCAAGCCCTTAGACGAGAAAAGATTTTGCGAGCTTAGGAGT

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	43.60%	1.90%	24.67%	29.75%	NA
All Indica	2759	26.90%	3.30%	37.98%	31.90%	NA
All Japonica	1512	69.80%	0.00%	3.44%	26.72%	NA
Aus	269	71.00%	0.70%	14.13%	14.13%	NA
Indica I	595	6.70%	3.90%	30.59%	58.82%	NA
Indica II	465	17.40%	4.90%	36.99%	40.65%	NA
Indica III	913	42.80%	1.50%	45.24%	10.41%	NA
Indica Intermediate	786	29.10%	3.80%	35.75%	31.30%	NA
Temperate Japonica	767	91.80%	0.00%	1.17%	7.04%	NA
Tropical Japonica	504	39.10%	0.00%	6.94%	53.97%	NA
Japonica Intermediate	241	64.30%	0.00%	3.32%	32.37%	NA
VI/Aromatic	96	20.80%	0.00%	15.62%	63.54%	NA
Intermediate	90	60.00%	0.00%	14.44%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1215354257	G -> DEL	N	N	silent_mutation	Average:10.848; most accessible tissue: Callus, score: 40.55	N	N	N	N
vg1215354257	G -> A	LOC_Os12g26310.1	intron_variant ; MODIFIER	silent_mutation	Average:10.848; most accessible tissue: Callus, score: 40.55	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1215354257	NA	1.04E-06	mr1020_2	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
vg1215354257	2.46E-06	NA	mr1136_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
vg1215354257	NA	5.34E-09	mr1198_2	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
vg1215354257	NA	2.28E-10	mr1228_2	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
vg1215354257	NA	1.09E-06	mr1275_2	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
vg1215354257	NA	4.17E-06	mr1407_2	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
vg1215354257	6.32E-06	6.32E-06	mr1407_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
vg1215354257	2.36E-06	2.36E-06	mr1511_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
vg1215354257	NA	7.61E-06	mr1557_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
vg1215354257	NA	7.49E-06	mr1704_2	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
vg1215354257	NA	3.85E-06	mr1873_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
vg1215354257	NA	5.34E-08	mr1885_2	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
vg1215354257	NA	1.70E-08	mr1940_2	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