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Detailed information for vg1202047032:

Variant ID: vg1202047032 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 2047032
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, G: 0.08, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

GTGCACTGCGCATACATTATTCCTGTGGTTAGTAATGTGTTACAGCTTTCACACTCTGCGAATCGGCGAAGTTGGTATTATTCTTTCGCTGGGCCGGGTT[G/C]
AACAGTGATGGGCTTTCCTTCGTGGGCTTGTCACTGTGCGGCCTGGTCAATGGGAATTTACCATTTCGCCTACCCTTATGACACGCGGCGGCTCGTGGTT

Reverse complement sequence

AACCACGAGCCGCCGCGTGTCATAAGGGTAGGCGAAATGGTAAATTCCCATTGACCAGGCCGCACAGTGACAAGCCCACGAAGGAAAGCCCATCACTGTT[C/G]
AACCCGGCCCAGCGAAAGAATAATACCAACTTCGCCGATTCGCAGAGTGTGAAAGCTGTAACACATTACTAACCACAGGAATAATGTATGCGCAGTGCAC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	38.30%	13.90%	18.87%	28.97%	NA
All Indica	2759	14.80%	6.30%	30.95%	47.88%	NA
All Japonica	1512	83.70%	13.40%	1.26%	1.65%	NA
Aus	269	1.90%	93.30%	2.60%	2.23%	NA
Indica I	595	26.40%	1.30%	36.97%	35.29%	NA
Indica II	465	15.30%	1.70%	36.56%	46.45%	NA
Indica III	913	7.00%	9.40%	25.30%	58.27%	NA
Indica Intermediate	786	14.90%	9.30%	29.64%	46.18%	NA
Temperate Japonica	767	87.70%	7.70%	1.96%	2.61%	NA
Tropical Japonica	504	89.30%	9.70%	0.20%	0.79%	NA
Japonica Intermediate	241	59.30%	39.00%	1.24%	0.41%	NA
VI/Aromatic	96	80.20%	16.70%	1.04%	2.08%	NA
Intermediate	90	57.80%	13.30%	12.22%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1202047032	G -> C	LOC_Os12g04810.1	upstream_gene_variant ; 4209.0bp to feature; MODIFIER	silent_mutation	Average:15.383; most accessible tissue: Callus, score: 67.025	N	N	N	N
vg1202047032	G -> C	LOC_Os12g04790.1	downstream_gene_variant ; 1556.0bp to feature; MODIFIER	silent_mutation	Average:15.383; most accessible tissue: Callus, score: 67.025	N	N	N	N
vg1202047032	G -> C	LOC_Os12g04800.1	intron_variant ; MODIFIER	silent_mutation	Average:15.383; most accessible tissue: Callus, score: 67.025	N	N	N	N
vg1202047032	G -> DEL	N	N	silent_mutation	Average:15.383; most accessible tissue: Callus, score: 67.025	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1202047032	NA	1.51E-07	mr1053	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
vg1202047032	1.68E-07	3.68E-12	mr1057	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
vg1202047032	NA	5.23E-06	mr1057	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
vg1202047032	NA	5.50E-06	mr1305	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
vg1202047032	NA	5.54E-08	mr1365	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
vg1202047032	NA	7.75E-06	mr1400	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
vg1202047032	NA	4.43E-06	mr1585	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
vg1202047032	NA	1.15E-07	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
vg1202047032	NA	6.36E-06	mr1118_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
vg1202047032	NA	2.00E-15	mr1794_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