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Detailed information for vg0321403368:

Variant ID: vg0321403368 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 21403368
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

AGCCATCAGAATAGCGTAAAGCATTTTCTGGGCCTGAGGGTATCGGGTCTTGGCGTCCCGAAGGGCCTCGCTAACAAATTAGACGGGCCGCTGCACCTTT[C/T]
GGCGGGGCCGATCCTCTTCGCTAGGGGCCGCATCAACGGGGCGCTCTTCGTCCGAGAGGCCGCGCACTCGGCTTCTGTGCCGATGACCTCGGGGTCGGAG

Reverse complement sequence

CTCCGACCCCGAGGTCATCGGCACAGAAGCCGAGTGCGCGGCCTCTCGGACGAAGAGCGCCCCGTTGATGCGGCCCCTAGCGAAGAGGATCGGCCCCGCC[G/A]
AAAGGTGCAGCGGCCCGTCTAATTTGTTAGCGAGGCCCTTCGGGACGCCAAGACCCGATACCCTCAGGCCCAGAAAATGCTTTACGCTATTCTGATGGCT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	76.60%	21.00%	1.65%	0.76%	NA
All Indica	2759	63.50%	32.80%	2.65%	1.01%	NA
All Japonica	1512	99.50%	0.10%	0.13%	0.26%	NA
Aus	269	69.90%	29.70%	0.37%	0.00%	NA
Indica I	595	42.20%	49.40%	8.24%	0.17%	NA
Indica II	465	89.70%	7.50%	0.43%	2.37%	NA
Indica III	913	59.50%	39.40%	0.55%	0.55%	NA
Indica Intermediate	786	68.80%	27.60%	2.16%	1.40%	NA
Temperate Japonica	767	99.70%	0.10%	0.13%	0.00%	NA
Tropical Japonica	504	99.00%	0.00%	0.20%	0.79%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	86.70%	7.80%	2.22%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0321403368	C -> T	LOC_Os03g38570.1	missense_variant ; p.Glu1325Lys; MODERATE	nonsynonymous_codon ; E1325K	Average:66.337; most accessible tissue: Zhenshan97 flag leaf, score: 80.373	unknown	unknown	DELETERIOUS	0.01
vg0321403368	C -> DEL	LOC_Os03g38570.1	N	frameshift_variant	Average:66.337; 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
vg0321403368	2.05E-06	NA	mr1102	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
vg0321403368	NA	1.21E-08	mr1659	Ind_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