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Detailed information for vg0614297874:

Variant ID: vg0614297874 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 14297874
Reference Allele: G	Alternative Allele: A,T
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGGAATCGTGTCTTGTGGGTACAGTGGTACATCTCTGGCCAGAGTAAAACTATTCGAATAGCCGTGCCCGCGGTTATGGGCGGGTCTAACAATGTTTTTC[G/A,T]
TGATTAGTCCCACACTACTCATTAATGATAACAATGTGATAATTAATTTGACTCCTGGTTTAGAATGGATAATTCCTGGTTTGGAGGTTTGATCTGTACG

Reverse complement sequence

CGTACAGATCAAACCTCCAAACCAGGAATTATCCATTCTAAACCAGGAGTCAAATTAATTATCACATTGTTATCATTAATGAGTAGTGTGGGACTAATCA[C/T,A]
GAAAAACATTGTTAGACCCGCCCATAACCGCGGGCACGGCTATTCGAATAGTTTTACTCTGGCCAGAGATGTACCACTGTACCCACAAGACACGATTCCA

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	87.60%	5.00%	6.79%	0.68%	NA
All Indica	2759	98.70%	0.30%	1.01%	0.04%	NA
All Japonica	1512	64.90%	14.60%	18.45%	1.98%	NA
Aus	269	98.90%	0.00%	1.12%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	98.70%	0.20%	1.08%	0.00%	NA
Indica III	913	99.70%	0.00%	0.33%	0.00%	NA
Indica Intermediate	786	96.60%	0.90%	2.42%	0.13%	NA
Temperate Japonica	767	95.30%	1.40%	3.26%	0.00%	NA
Tropical Japonica	504	24.00%	29.60%	40.67%	5.75%	NA
Japonica Intermediate	241	53.90%	25.30%	20.33%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	80.00%	6.70%	12.22%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0614297874	G -> T	LOC_Os06g24420.1	upstream_gene_variant ; 4038.0bp to feature; MODIFIER	N	Average:60.814; most accessible tissue: Minghui63 panicle, score: 81.412	N	N	N	N
vg0614297874	G -> T	LOC_Os06g24404-LOC_Os06g24420	intergenic_region ; MODIFIER	N	Average:60.814; most accessible tissue: Minghui63 panicle, score: 81.412	N	N	N	N
vg0614297874	G -> A	LOC_Os06g24420.1	upstream_gene_variant ; 4038.0bp to feature; MODIFIER	silent_mutation	Average:60.814; most accessible tissue: Minghui63 panicle, score: 81.412	N	N	N	N
vg0614297874	G -> A	LOC_Os06g24404-LOC_Os06g24420	intergenic_region ; MODIFIER	silent_mutation	Average:60.814; most accessible tissue: Minghui63 panicle, score: 81.412	N	N	N	N
vg0614297874	G -> DEL	N	N	silent_mutation	Average:60.814; most accessible tissue: Minghui63 panicle, score: 81.412	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0614297874	NA	8.27E-06	mr1448	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
vg0614297874	NA	5.43E-09	mr1593	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
vg0614297874	NA	1.59E-20	mr1593	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
vg0614297874	NA	6.85E-29	mr1699	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
vg0614297874	NA	8.34E-12	mr1871	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
vg0614297874	NA	2.52E-17	mr1062_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
vg0614297874	NA	1.49E-12	mr1097_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
vg0614297874	NA	3.98E-07	mr1250_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
vg0614297874	NA	1.41E-06	mr1363_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
vg0614297874	NA	2.08E-06	mr1423_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
vg0614297874	NA	8.62E-13	mr1593_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
vg0614297874	NA	8.94E-24	mr1593_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
vg0614297874	NA	3.66E-31	mr1699_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
vg0614297874	NA	1.40E-12	mr1742_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
vg0614297874	NA	2.72E-07	mr1786_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