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Detailed information for vg1218796192:

Variant ID: vg1218796192 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 18796192
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTATGGGGTACCCATAATATCCACAAAACCTATCTCAACCAAATTATTAAGGCCCTGTTTGTTTCAGTTTAAGATTATTGTAATCTAGATTGTTAAATCA[G/A]
ATTACTCTAAGCTGGATTATAATAAGCTGACATAAAATAAGCTATGTGTTGTTTGTTTCTCTGGATTATTAGAGACATTTAAGGGTAGTGAGTCTTTAGC

Reverse complement sequence

GCTAAAGACTCACTACCCTTAAATGTCTCTAATAATCCAGAGAAACAAACAACACATAGCTTATTTTATGTCAGCTTATTATAATCCAGCTTAGAGTAAT[C/T]
TGATTTAACAATCTAGATTACAATAATCTTAAACTGAAACAAACAGGGCCTTAATAATTTGGTTGAGATAGGTTTTGTGGATATTATGGGTACCCCATAC

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	55.70%	21.60%	0.34%	22.34%	NA
All Indica	2759	70.90%	3.10%	0.40%	25.59%	NA
All Japonica	1512	38.10%	55.70%	0.20%	6.02%	NA
Aus	269	20.10%	0.40%	0.37%	79.18%	NA
Indica I	595	76.30%	3.20%	0.17%	20.34%	NA
Indica II	465	86.90%	0.90%	0.00%	12.26%	NA
Indica III	913	65.30%	2.70%	0.33%	31.65%	NA
Indica Intermediate	786	63.90%	4.80%	0.89%	30.41%	NA
Temperate Japonica	767	64.30%	34.70%	0.13%	0.91%	NA
Tropical Japonica	504	3.20%	91.90%	0.40%	4.56%	NA
Japonica Intermediate	241	27.80%	46.90%	0.00%	25.31%	NA
VI/Aromatic	96	6.20%	61.50%	0.00%	32.29%	NA
Intermediate	90	45.60%	36.70%	1.11%	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
vg1218796192	G -> DEL	N	N	silent_mutation	Average:31.048; most accessible tissue: Callus, score: 59.294	N	N	N	N
vg1218796192	G -> A	LOC_Os12g31210.1	upstream_gene_variant ; 3410.0bp to feature; MODIFIER	silent_mutation	Average:31.048; most accessible tissue: Callus, score: 59.294	N	N	N	N
vg1218796192	G -> A	LOC_Os12g31210-LOC_Os12g31230	intergenic_region ; MODIFIER	silent_mutation	Average:31.048; most accessible tissue: Callus, score: 59.294	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1218796192	NA	5.10E-10	mr1128	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
vg1218796192	NA	8.74E-06	mr1418	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
vg1218796192	NA	7.69E-14	mr1521	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
vg1218796192	NA	1.83E-06	mr1646	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
vg1218796192	NA	2.21E-07	mr1729	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
vg1218796192	NA	5.97E-09	mr1779	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
vg1218796192	NA	2.45E-07	mr1797	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
vg1218796192	NA	2.45E-07	mr1801	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
vg1218796192	NA	1.46E-06	mr1851	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
vg1218796192	NA	1.89E-12	mr1864	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
vg1218796192	NA	5.89E-08	mr1084_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
vg1218796192	NA	2.65E-11	mr1097_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
vg1218796192	NA	6.88E-06	mr1458_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
vg1218796192	NA	3.61E-14	mr1521_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
vg1218796192	NA	8.53E-08	mr1563_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