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Detailed information for vg0621415002:

Variant ID: vg0621415002 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 21415002
Reference Allele: C	Alternative Allele: G
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, C: 0.00, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

ATATTTATCAATACTCCTGATTATTAGACTAACATTCAATCACTTTGTCGGAAAGGTGTCGGTAAACAATGATCGCGGTGATGATTTCGCATCAATCCGC[C/G]
TGAGCAACCGACGGTTAACTAACCTTCCTTGTGATGTCACCTTTGTTTTTCCTCTCCTTTTTCTTTTTCTGTCTCTCCCTTTTGCTTTGCTTCAATATCA

Reverse complement sequence

TGATATTGAAGCAAAGCAAAAGGGAGAGACAGAAAAAGAAAAAGGAGAGGAAAAACAAAGGTGACATCACAAGGAAGGTTAGTTAACCGTCGGTTGCTCA[G/C]
GCGGATTGATGCGAAATCATCACCGCGATCATTGTTTACCGACACCTTTCCGACAAAGTGATTGAATGTTAGTCTAATAATCAGGAGTATTGATAAATAT

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	69.20%	30.70%	0.08%	0.00%	NA
All Indica	2759	98.70%	1.30%	0.00%	0.00%	NA
All Japonica	1512	10.10%	89.60%	0.26%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	97.60%	2.40%	0.00%	0.00%	NA
Indica III	913	99.50%	0.50%	0.00%	0.00%	NA
Indica Intermediate	786	97.70%	2.30%	0.00%	0.00%	NA
Temperate Japonica	767	7.20%	92.30%	0.52%	0.00%	NA
Tropical Japonica	504	15.70%	84.30%	0.00%	0.00%	NA
Japonica Intermediate	241	7.90%	92.10%	0.00%	0.00%	NA
VI/Aromatic	96	78.10%	21.90%	0.00%	0.00%	NA
Intermediate	90	58.90%	41.10%	0.00%	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
vg0621415002	C -> G	LOC_Os06g36470.1	downstream_gene_variant ; 4679.0bp to feature; MODIFIER	silent_mutation	Average:53.151; most accessible tissue: Callus, score: 94.199	N	N	N	N
vg0621415002	C -> G	LOC_Os06g36480.1	intron_variant ; MODIFIER	silent_mutation	Average:53.151; most accessible tissue: Callus, score: 94.199	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0621415002	NA	1.64E-15	mr1010	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
vg0621415002	3.28E-07	2.02E-07	mr1010	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
vg0621415002	NA	1.13E-21	mr1163	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
vg0621415002	7.89E-06	7.89E-06	mr1267	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
vg0621415002	NA	1.03E-06	mr1690	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
vg0621415002	NA	4.24E-25	mr1024_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
vg0621415002	NA	1.27E-19	mr1276_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
vg0621415002	NA	1.24E-06	mr1369_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
vg0621415002	NA	2.99E-07	mr1453_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
vg0621415002	8.08E-06	NA	mr1842_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