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Detailed information for vg0614236515:

Variant ID: vg0614236515 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 14236515
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATCGACAACAGCGTCAACACCGGCATCAACTAAGGAGTTTCTACTTCAACAATGCTAGTGTAGACTCAAGTCGGCGAAATTGTCTTCCCGGTTTACACCA[C/T]
GATGCCGATCTTGACTGATCCATCAATGACCGGAAGCGAGAACGCCGTGGTTACAACCCTGGGCGACTCCATGTCGAAGGATCCTCCCGCATAAGTGGAG

Reverse complement sequence

CTCCACTTATGCGGGAGGATCCTTCGACATGGAGTCGCCCAGGGTTGTAACCACGGCGTTCTCGCTTCCGGTCATTGATGGATCAGTCAAGATCGGCATC[G/A]
TGGTGTAAACCGGGAAGACAATTTCGCCGACTTGAGTCTACACTAGCATTGTTGAAGTAGAAACTCCTTAGTTGATGCCGGTGTTGACGCTGTTGTCGAT

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	92.40%	7.20%	0.44%	0.00%	NA
All Indica	2759	98.90%	1.10%	0.04%	0.00%	NA
All Japonica	1512	79.40%	19.40%	1.26%	0.00%	NA
Aus	269	98.90%	1.10%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	98.70%	1.30%	0.00%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	97.30%	2.70%	0.00%	0.00%	NA
Temperate Japonica	767	98.20%	1.60%	0.26%	0.00%	NA
Tropical Japonica	504	46.60%	51.40%	1.98%	0.00%	NA
Japonica Intermediate	241	88.00%	9.10%	2.90%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	83.30%	15.60%	1.11%	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
vg0614236515	C -> T	LOC_Os06g24310-LOC_Os06g24350	intergenic_region ; MODIFIER	silent_mutation	Average:45.029; most accessible tissue: Minghui63 flag leaf, score: 71.116	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0614236515	NA	1.02E-06	mr1243	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
vg0614236515	1.08E-07	7.58E-26	mr1301	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
vg0614236515	NA	1.17E-15	mr1301	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
vg0614236515	2.93E-10	1.45E-22	mr1410	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
vg0614236515	NA	9.94E-17	mr1410	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
vg0614236515	NA	7.94E-07	mr1993	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
vg0614236515	3.92E-07	3.55E-25	mr1301_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
vg0614236515	NA	4.78E-17	mr1301_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
vg0614236515	3.45E-09	5.94E-22	mr1410_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
vg0614236515	NA	4.86E-16	mr1410_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
vg0614236515	NA	4.09E-11	mr1993_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
vg0614236515	NA	1.13E-11	mr1993_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