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Detailed information for vg1217063939:

Variant ID: vg1217063939 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 17063939
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTATCATACATGGGTCCCATATTTTTTTAATAAATAAAATGCTGACTGGATTGCTACGCGTACGCCACGTAGGACAAAACCGCTCTGAATTGGGTCGAGG[G/A]
GGTAATTTGTCCGGTATTGAAAGTTGAGGGTGAACGATGTCTGGTTTTCGGGTTTAGAGGGGTAATTCGGTCGACCGCGATAGTTCAGGAGGTAATTCGA

Reverse complement sequence

TCGAATTACCTCCTGAACTATCGCGGTCGACCGAATTACCCCTCTAAACCCGAAAACCAGACATCGTTCACCCTCAACTTTCAATACCGGACAAATTACC[C/T]
CCTCGACCCAATTCAGAGCGGTTTTGTCCTACGTGGCGTACGCGTAGCAATCCAGTCAGCATTTTATTTATTAAAAAAATATGGGACCCATGTATGATAC

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	74.70%	7.30%	0.44%	17.60%	NA
All Indica	2759	82.00%	1.10%	0.36%	16.56%	NA
All Japonica	1512	74.00%	18.80%	0.26%	6.88%	NA
Aus	269	12.30%	7.80%	1.86%	78.07%	NA
Indica I	595	94.50%	0.30%	0.17%	5.04%	NA
Indica II	465	71.20%	1.30%	0.22%	27.31%	NA
Indica III	913	82.70%	0.30%	0.44%	16.54%	NA
Indica Intermediate	786	78.20%	2.30%	0.51%	18.96%	NA
Temperate Japonica	767	79.30%	18.10%	0.26%	2.35%	NA
Tropical Japonica	504	76.60%	12.30%	0.20%	10.91%	NA
Japonica Intermediate	241	51.90%	34.90%	0.41%	12.86%	NA
VI/Aromatic	96	44.80%	1.00%	2.08%	52.08%	NA
Intermediate	90	78.90%	8.90%	0.00%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1217063939	G -> DEL	N	N	silent_mutation	Average:58.016; most accessible tissue: Minghui63 panicle, score: 79.811	N	N	N	N
vg1217063939	G -> A	LOC_Os12g28860.1	upstream_gene_variant ; 371.0bp to feature; MODIFIER	silent_mutation	Average:58.016; most accessible tissue: Minghui63 panicle, score: 79.811	N	N	N	N
vg1217063939	G -> A	LOC_Os12g28870.1	upstream_gene_variant ; 667.0bp to feature; MODIFIER	silent_mutation	Average:58.016; most accessible tissue: Minghui63 panicle, score: 79.811	N	N	N	N
vg1217063939	G -> A	LOC_Os12g28860-LOC_Os12g28870	intergenic_region ; MODIFIER	silent_mutation	Average:58.016; most accessible tissue: Minghui63 panicle, score: 79.811	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1217063939	NA	7.27E-06	mr1503	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
vg1217063939	7.58E-07	NA	mr1019_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
vg1217063939	3.89E-06	NA	mr1132_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
vg1217063939	2.40E-06	NA	mr1137_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
vg1217063939	NA	1.00E-08	mr1137_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
vg1217063939	1.44E-07	NA	mr1178_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
vg1217063939	NA	5.10E-07	mr1183_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
vg1217063939	NA	1.18E-06	mr1617_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
vg1217063939	NA	2.24E-06	mr1691_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
vg1217063939	NA	1.74E-06	mr1705_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