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Detailed information for vg0618978160:

Variant ID: vg0618978160 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 18978160
Reference Allele: G	Alternative Allele: C
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, C: 0.02, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:

CATGTTGCCGATGCATGGTCCTGTGCATGCTGGTGATCACGTGTCATCGTATCATTTGTCGGCCATGTTGCCATTCACAGCCTTGTTGAATTTGGTTGTT[G/C]
ATGATGTCGCCGGTGGCGAAGACGATGCAACCCGCCCGACTAGTTGACGATGACGGCGCGGCCGCGCGGGCACAGGCCCGTGCACAAGTCTGGCAGCAGC

Reverse complement sequence

GCTGCTGCCAGACTTGTGCACGGGCCTGTGCCCGCGCGGCCGCGCCGTCATCGTCAACTAGTCGGGCGGGTTGCATCGTCTTCGCCACCGGCGACATCAT[C/G]
AACAACCAAATTCAACAAGGCTGTGAATGGCAACATGGCCGACAAATGATACGATGACACGTGATCACCAGCATGCACAGGACCATGCATCGGCAACATG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	48.10%	45.60%	0.72%	5.59%	NA
All Indica	2759	75.80%	19.60%	0.43%	4.17%	NA
All Japonica	1512	2.60%	91.90%	1.12%	4.37%	NA
Aus	269	37.20%	62.80%	0.00%	0.00%	NA
Indica I	595	78.80%	19.30%	1.01%	0.84%	NA
Indica II	465	92.00%	6.50%	0.22%	1.29%	NA
Indica III	913	69.40%	21.70%	0.11%	8.76%	NA
Indica Intermediate	786	71.20%	25.20%	0.51%	3.05%	NA
Temperate Japonica	767	3.80%	89.20%	1.96%	5.08%	NA
Tropical Japonica	504	0.80%	98.20%	0.20%	0.79%	NA
Japonica Intermediate	241	2.90%	87.10%	0.41%	9.54%	NA
VI/Aromatic	96	4.20%	19.80%	2.08%	73.96%	NA
Intermediate	90	42.20%	41.10%	3.33%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0618978160	G -> C	LOC_Os06g32630.1	intron_variant ; MODIFIER	silent_mutation	Average:65.755; most accessible tissue: Zhenshan97 flag leaf, score: 80.373	N	N	N	N
vg0618978160	G -> DEL	N	N	silent_mutation	Average:65.755; most accessible tissue: Zhenshan97 flag leaf, score: 80.373	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0618978160	NA	9.55E-06	mr1129	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
vg0618978160	NA	4.45E-11	mr1138	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
vg0618978160	NA	1.65E-09	mr1354	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
vg0618978160	NA	3.91E-08	mr1398	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
vg0618978160	NA	2.87E-09	mr1770	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
vg0618978160	NA	3.86E-07	mr1042_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
vg0618978160	NA	6.64E-06	mr1043_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
vg0618978160	NA	2.48E-06	mr1094_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
vg0618978160	NA	8.92E-10	mr1172_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
vg0618978160	NA	5.96E-06	mr1269_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
vg0618978160	NA	7.12E-06	mr1346_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
vg0618978160	NA	7.18E-09	mr1354_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
vg0618978160	NA	8.17E-06	mr1428_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
vg0618978160	NA	1.72E-06	mr1479_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
vg0618978160	NA	2.61E-08	mr1681_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