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Detailed information for vg0321827246:

Variant ID: vg0321827246 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 21827246
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGGTATTGGCACATCATGAGACCCCACTTTGATGGTAATTACTTCTGAAGTCCTTGCCTCCACCTTGACGCGCTTTCCTTCCCTCTTTTCTTCATTAGCC[C/T]
GATTCTTACCATAAAACCGGCTATTGTTTGGTGAAGACAAACGCTCATGAATTGGCCTCCTCGGTCCTCCCCACCCTTGGTTGAATTGCATTGGAGGCAT

Reverse complement sequence

ATGCCTCCAATGCAATTCAACCAAGGGTGGGGAGGACCGAGGAGGCCAATTCATGAGCGTTTGTCTTCACCAAACAATAGCCGGTTTTATGGTAAGAATC[G/A]
GGCTAATGAAGAAAAGAGGGAAGGAAAGCGCGTCAAGGTGGAGGCAAGGACTTCAGAAGTAATTACCATCAAAGTGGGGTCTCATGATGTGCCAATACCT

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	91.60%	2.60%	5.82%	0.02%	NA
All Indica	2759	87.40%	3.90%	8.63%	0.04%	NA
All Japonica	1512	98.50%	0.50%	0.99%	0.00%	NA
Aus	269	91.40%	1.50%	7.06%	0.00%	NA
Indica I	595	96.80%	0.50%	2.52%	0.17%	NA
Indica II	465	76.80%	6.50%	16.77%	0.00%	NA
Indica III	913	85.20%	5.30%	9.53%	0.00%	NA
Indica Intermediate	786	89.20%	3.40%	7.38%	0.00%	NA
Temperate Japonica	767	97.70%	0.70%	1.69%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	0.40%	0.83%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	3.30%	3.33%	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
vg0321827246	C -> T	LOC_Os03g39284.1	missense_variant ; p.Arg763Gln; MODERATE	nonsynonymous_codon ; R763Q	Average:23.955; most accessible tissue: Zhenshan97 panicle, score: 39.652	benign	0.575	TOLERATED	0.10
vg0321827246	C -> DEL	LOC_Os03g39284.1	N	frameshift_variant	Average:23.955; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0321827246	1.79E-06	5.10E-10	mr1174	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
vg0321827246	NA	8.49E-08	mr1347_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