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Detailed information for vg1201180694:

Variant ID: vg1201180694 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 1180694
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGCATCGGCGGCCACGCCGTCGACGGCTGCCGGGAGTTCATGGCGTCGGGCGCCGATGGCACCGCCGCCGCGCTCCTCTGCGCCGCCTGCGGCTGCCACC[A/G]
GAGCTTCCACAGGCGAGAGGTGGAGGCCGCCGCGGCCGAATGCGACTGCTCCTCCGACACCTCCTCCGGCACCGGCCGCCGGTGATCGCCGTGGATTTGA

Reverse complement sequence

TCAAATCCACGGCGATCACCGGCGGCCGGTGCCGGAGGAGGTGTCGGAGGAGCAGTCGCATTCGGCCGCGGCGGCCTCCACCTCTCGCCTGTGGAAGCTC[T/C]
GGTGGCAGCCGCAGGCGGCGCAGAGGAGCGCGGCGGCGGTGCCATCGGCGCCCGACGCCATGAACTCCCGGCAGCCGTCGACGGCGTGGCCGCCGATGCT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	67.40%	31.20%	1.33%	0.00%	NA
All Indica	2759	63.20%	36.60%	0.22%	0.00%	NA
All Japonica	1512	88.00%	8.90%	3.17%	0.00%	NA
Aus	269	1.10%	98.90%	0.00%	0.00%	NA
Indica I	595	58.80%	41.00%	0.17%	0.00%	NA
Indica II	465	90.30%	9.20%	0.43%	0.00%	NA
Indica III	913	53.70%	46.30%	0.00%	0.00%	NA
Indica Intermediate	786	61.60%	38.00%	0.38%	0.00%	NA
Temperate Japonica	767	90.70%	5.10%	4.17%	0.00%	NA
Tropical Japonica	504	80.80%	16.90%	2.38%	0.00%	NA
Japonica Intermediate	241	94.20%	4.10%	1.66%	0.00%	NA
VI/Aromatic	96	39.60%	56.20%	4.17%	0.00%	NA
Intermediate	90	80.00%	14.40%	5.56%	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
vg1201180694	A -> G	LOC_Os12g03110.1	missense_variant ; p.Gln78Arg; MODERATE	nonsynonymous_codon ; Q78R	Average:58.05; most accessible tissue: Minghui63 panicle, score: 85.556	possibly damaging	-1.945	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1201180694	NA	1.34E-06	mr1038	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
vg1201180694	NA	5.53E-06	mr1201	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
vg1201180694	8.90E-08	9.19E-09	mr1219	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
vg1201180694	8.05E-07	5.69E-07	mr1274	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
vg1201180694	NA	9.89E-07	mr1545	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
vg1201180694	NA	8.36E-06	mr1201_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
vg1201180694	1.34E-06	2.92E-07	mr1219_2	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
vg1201180694	7.51E-06	2.63E-06	mr1274_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
vg1201180694	7.43E-07	7.43E-07	mr1587_2	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
vg1201180694	NA	3.34E-06	mr1591_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
vg1201180694	7.15E-06	3.27E-06	mr1594_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
vg1201180694	NA	1.95E-08	mr1829_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
vg1201180694	3.86E-06	7.02E-08	mr1842_2	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
vg1201180694	NA	1.72E-07	mr1902_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