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Detailed information for vg0614842115:

Variant ID: vg0614842115 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 14842115
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAACATCATGTCAACCATGCGCCGTGATACTTAACAAGTACCCGAATAGAGATTGTGACAATGCCCTCTATATAATACAATTCAAAGTAGTGCACCATTC[C/T]
CGGATCATAATCACCCCCTTATAAACAAGGTATGGACTCCCCAGCGACCCCCGTGGGCTTATCTCCGCCACTTCACAGTCTGGTACTCTACAATGAACCA

Reverse complement sequence

TGGTTCATTGTAGAGTACCAGACTGTGAAGTGGCGGAGATAAGCCCACGGGGGTCGCTGGGGAGTCCATACCTTGTTTATAAGGGGGTGATTATGATCCG[G/A]
GAATGGTGCACTACTTTGAATTGTATTATATAGAGGGCATTGTCACAATCTCTATTCGGGTACTTGTTAAGTATCACGGCGCATGGTTGACATGATGTTG

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	56.40%	0.10%	8.68%	34.83%	NA
All Indica	2759	32.20%	0.10%	13.59%	54.11%	NA
All Japonica	1512	94.20%	0.10%	0.86%	4.83%	NA
Aus	269	76.60%	0.00%	5.20%	18.22%	NA
Indica I	595	38.00%	0.00%	5.71%	56.30%	NA
Indica II	465	34.80%	0.20%	14.62%	50.32%	NA
Indica III	913	20.30%	0.00%	18.84%	60.90%	NA
Indica Intermediate	786	40.10%	0.30%	12.85%	46.82%	NA
Temperate Japonica	767	96.90%	0.00%	0.91%	2.22%	NA
Tropical Japonica	504	89.30%	0.00%	0.60%	10.12%	NA
Japonica Intermediate	241	96.30%	0.40%	1.24%	2.07%	NA
VI/Aromatic	96	90.60%	0.00%	0.00%	9.38%	NA
Intermediate	90	66.70%	0.00%	8.89%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0614842115	C -> T	LOC_Os06g25330.1	downstream_gene_variant ; 3829.0bp to feature; MODIFIER	silent_mutation	Average:18.684; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N
vg0614842115	C -> T	LOC_Os06g25340.1	intron_variant ; MODIFIER	silent_mutation	Average:18.684; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N
vg0614842115	C -> DEL	N	N	silent_mutation	Average:18.684; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0614842115	NA	3.81E-06	mr1113	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
vg0614842115	NA	4.25E-06	mr1114	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
vg0614842115	NA	2.33E-08	mr1116	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
vg0614842115	2.07E-06	9.28E-10	mr1119	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
vg0614842115	5.46E-06	4.38E-08	mr1247	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
vg0614842115	NA	4.20E-11	mr1495	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
vg0614842115	NA	9.86E-06	mr1917	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
vg0614842115	NA	7.73E-06	mr1113_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
vg0614842115	NA	6.68E-06	mr1114_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
vg0614842115	NA	3.70E-06	mr1117_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
vg0614842115	NA	3.92E-11	mr1118_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
vg0614842115	NA	4.67E-06	mr1119_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
vg0614842115	NA	3.08E-07	mr1120_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
vg0614842115	NA	4.74E-07	mr1247_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
vg0614842115	NA	5.23E-06	mr1258_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