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Detailed information for vg0402471059:

Variant ID: vg0402471059 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 2471059
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTGGTATTAATGTATGATAAATTGAGTTTTAATTATTAAAACTTAAAAAAATAGATTAATATGATATTTTAGAGCAACTTTCATATAGAAAATTTTCGCA[C/T]
GAAATGCACCGTTTAACAGTTTGAAAAGCGTGCCACGAAAATCTTAATCTTCATTCAACTCTTGTTGGAGAAAAGAATGAGACACATATATGATTGATAT

Reverse complement sequence

ATATCAATCATATATGTGTCTCATTCTTTTCTCCAACAAGAGTTGAATGAAGATTAAGATTTTCGTGGCACGCTTTTCAAACTGTTAAACGGTGCATTTC[G/A]
TGCGAAAATTTTCTATATGAAAGTTGCTCTAAAATATCATATTAATCTATTTTTTTAAGTTTTAATAATTAAAACTCAATTTATCATACATTAATACCAC

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	90.90%	7.80%	0.13%	1.23%	NA
All Indica	2759	90.30%	7.40%	0.22%	2.10%	NA
All Japonica	1512	90.60%	9.40%	0.00%	0.00%	NA
Aus	269	94.10%	5.90%	0.00%	0.00%	NA
Indica I	595	98.80%	1.20%	0.00%	0.00%	NA
Indica II	465	97.20%	0.90%	0.00%	1.94%	NA
Indica III	913	81.30%	14.50%	0.44%	3.83%	NA
Indica Intermediate	786	90.10%	7.90%	0.25%	1.78%	NA
Temperate Japonica	767	99.20%	0.80%	0.00%	0.00%	NA
Tropical Japonica	504	84.10%	15.90%	0.00%	0.00%	NA
Japonica Intermediate	241	76.80%	23.20%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0402471059	C -> DEL	N	N	silent_mutation	Average:41.845; most accessible tissue: Zhenshan97 panicle, score: 76.605	N	N	N	N
vg0402471059	C -> T	LOC_Os04g05040-LOC_Os04g05050	intergenic_region ; MODIFIER	silent_mutation	Average:41.845; most accessible tissue: Zhenshan97 panicle, score: 76.605	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0402471059	NA	2.96E-06	mr1380	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
vg0402471059	NA	3.76E-06	mr1561	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
vg0402471059	2.12E-06	1.50E-08	mr1561	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
vg0402471059	NA	1.88E-10	mr1798	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
vg0402471059	NA	8.16E-06	mr1971	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
vg0402471059	NA	2.38E-06	mr1181_2	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
vg0402471059	NA	4.07E-07	mr1380_2	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
vg0402471059	NA	1.91E-07	mr1561_2	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
vg0402471059	NA	6.60E-06	mr1642_2	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
vg0402471059	NA	6.88E-09	mr1653_2	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
vg0402471059	NA	6.39E-07	mr1676_2	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
vg0402471059	NA	1.09E-06	mr1708_2	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
vg0402471059	2.11E-06	1.62E-16	mr1798_2	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
vg0402471059	NA	1.66E-06	mr1996_2	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