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Detailed information for vg0604130041:

Variant ID: vg0604130041 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 4130041
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCCCTTCTTTTTCAGCTCAGGCAACCTCCTTATCTTCTCCGGCGCTAGCGGCATCCCTAAACTTTGGTAGGGACCTACAGATTAGGGTCTCGGTTGGGGT[C/T]
AAGGTGGAAGGGGGAAGAGGGGGGGGGGAGTTTGCCTATTTTAGAGGGATGGCCACGTGAGGTGGCAGTCCGGCGGTGAGTAGCGGATTGGGCAGGTGGC

Reverse complement sequence

GCCACCTGCCCAATCCGCTACTCACCGCCGGACTGCCACCTCACGTGGCCATCCCTCTAAAATAGGCAAACTCCCCCCCCCCTCTTCCCCCTTCCACCTT[G/A]
ACCCCAACCGAGACCCTAATCTGTAGGTCCCTACCAAAGTTTAGGGATGCCGCTAGCGCCGGAGAAGATAAGGAGGTTGCCTGAGCTGAAAAAGAAGGGC

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	76.50%	23.20%	0.28%	0.00%	NA
All Indica	2759	80.90%	19.00%	0.11%	0.00%	NA
All Japonica	1512	83.90%	15.80%	0.26%	0.00%	NA
Aus	269	1.90%	97.40%	0.74%	0.00%	NA
Indica I	595	80.20%	19.50%	0.34%	0.00%	NA
Indica II	465	97.20%	2.80%	0.00%	0.00%	NA
Indica III	913	74.20%	25.80%	0.00%	0.00%	NA
Indica Intermediate	786	79.50%	20.40%	0.13%	0.00%	NA
Temperate Japonica	767	98.70%	1.30%	0.00%	0.00%	NA
Tropical Japonica	504	64.90%	34.30%	0.79%	0.00%	NA
Japonica Intermediate	241	76.80%	23.20%	0.00%	0.00%	NA
VI/Aromatic	96	44.80%	55.20%	0.00%	0.00%	NA
Intermediate	90	74.40%	21.10%	4.44%	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
vg0604130041	C -> T	LOC_Os06g08420-LOC_Os06g08440	intergenic_region ; MODIFIER	silent_mutation	Average:52.933; most accessible tissue: Zhenshan97 panicle, score: 85.254	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0604130041	NA	4.06E-06	mr1057	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
vg0604130041	NA	4.01E-06	mr1262	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
vg0604130041	NA	8.35E-06	mr1283	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
vg0604130041	NA	1.26E-06	mr1345	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
vg0604130041	NA	5.95E-06	mr1373	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
vg0604130041	NA	6.02E-06	mr1417	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
vg0604130041	NA	1.18E-06	mr1485	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
vg0604130041	8.11E-06	8.10E-06	mr1485	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
vg0604130041	NA	5.49E-06	mr1512	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
vg0604130041	NA	2.26E-06	mr1759	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
vg0604130041	NA	5.62E-06	mr1774	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
vg0604130041	8.34E-06	6.97E-07	mr1920	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
vg0604130041	2.53E-06	2.53E-06	mr1853_2	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
vg0604130041	NA	1.12E-06	mr1888_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