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Detailed information for vg0619331736:

Variant ID: vg0619331736 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 19331736
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAAGTAGGATTTTAAAATATACAAACAAGAAAAATGCCGGGATTGGCTGCCATGCTCTTATAGAACCCGCAATAATTTCAAAACACAGGAATATATACAA[T/G]
AATATGACTTTGGATGGTTCACTTGAAATAAACATAGGAATTTTTTAGGAAGTTTATTTGGGTCATAGAGAGATCAGGGGGGGAGGGGGGTAGAGAATGC

Reverse complement sequence

GCATTCTCTACCCCCCTCCCCCCCTGATCTCTCTATGACCCAAATAAACTTCCTAAAAAATTCCTATGTTTATTTCAAGTGAACCATCCAAAGTCATATT[A/C]
TTGTATATATTCCTGTGTTTTGAAATTATTGCGGGTTCTATAAGAGCATGGCAGCCAATCCCGGCATTTTTCTTGTTTGTATATTTTAAAATCCTACTTT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	75.20%	24.70%	0.17%	0.00%	NA
All Indica	2759	80.70%	19.10%	0.22%	0.00%	NA
All Japonica	1512	77.10%	22.80%	0.07%	0.00%	NA
Aus	269	34.20%	65.80%	0.00%	0.00%	NA
Indica I	595	81.30%	18.50%	0.17%	0.00%	NA
Indica II	465	97.40%	2.20%	0.43%	0.00%	NA
Indica III	913	71.30%	28.60%	0.11%	0.00%	NA
Indica Intermediate	786	81.20%	18.60%	0.25%	0.00%	NA
Temperate Japonica	767	67.10%	32.70%	0.13%	0.00%	NA
Tropical Japonica	504	92.30%	7.70%	0.00%	0.00%	NA
Japonica Intermediate	241	77.20%	22.80%	0.00%	0.00%	NA
VI/Aromatic	96	1.00%	97.90%	1.04%	0.00%	NA
Intermediate	90	75.60%	24.40%	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
vg0619331736	T -> G	LOC_Os06g33200.1	downstream_gene_variant ; 2086.0bp to feature; MODIFIER	silent_mutation	Average:28.878; most accessible tissue: Callus, score: 64.383	N	N	N	N
vg0619331736	T -> G	LOC_Os06g33190-LOC_Os06g33200	intergenic_region ; MODIFIER	silent_mutation	Average:28.878; most accessible tissue: Callus, score: 64.383	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0619331736	NA	5.46E-19	Awn_length	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0619331736	NA	2.84E-06	mr1676	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
vg0619331736	NA	2.96E-08	mr1057_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
vg0619331736	NA	8.55E-07	mr1062_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
vg0619331736	NA	5.21E-12	mr1126_2	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
vg0619331736	NA	2.70E-06	mr1167_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
vg0619331736	NA	3.98E-06	mr1268_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
vg0619331736	NA	2.95E-06	mr1346_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
vg0619331736	NA	1.05E-07	mr1456_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
vg0619331736	NA	8.45E-06	mr1577_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
vg0619331736	NA	4.80E-08	mr1624_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
vg0619331736	NA	2.91E-06	mr1726_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
vg0619331736	NA	5.86E-06	mr1736_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
vg0619331736	NA	6.22E-06	mr1740_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
vg0619331736	NA	6.08E-06	mr1741_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
vg0619331736	NA	1.19E-07	mr1780_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
vg0619331736	NA	2.40E-06	mr1792_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
vg0619331736	NA	1.36E-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