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Detailed information for vg0901628621:

Variant ID: vg0901628621 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 1628621
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACCTCCACGTAGAGCGGATCTTCCGAAGCTGCGGCGTCTACACGACCAACGGAAAGGAAAAAGGCTTTTACTCTAATAAACTCCATATAACGAGCAGGAA[C/T]
AAAGCACAAAAATAGGTTCTTAACTTCTTAAGGGAAAATTAGAGACTTGAACGGTCCAATTCCGAGTTCAAATGGCCAAGTTATGGCCATTTGAAGTTTA

Reverse complement sequence

TAAACTTCAAATGGCCATAACTTGGCCATTTGAACTCGGAATTGGACCGTTCAAGTCTCTAATTTTCCCTTAAGAAGTTAAGAACCTATTTTTGTGCTTT[G/A]
TTCCTGCTCGTTATATGGAGTTTATTAGAGTAAAAGCCTTTTTCCTTTCCGTTGGTCGTGTAGACGCCGCAGCTTCGGAAGATCCGCTCTACGTGGAGGT

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	22.80%	8.80%	19.53%	48.88%	NA
All Indica	2759	3.00%	1.20%	21.86%	73.98%	NA
All Japonica	1512	64.60%	21.60%	7.67%	6.22%	NA
Aus	269	0.40%	0.40%	54.28%	44.98%	NA
Indica I	595	5.70%	0.70%	11.76%	81.85%	NA
Indica II	465	1.90%	0.00%	16.34%	81.72%	NA
Indica III	913	1.10%	1.40%	31.33%	66.16%	NA
Indica Intermediate	786	3.70%	2.00%	21.76%	72.52%	NA
Temperate Japonica	767	97.00%	0.80%	1.17%	1.04%	NA
Tropical Japonica	504	21.60%	49.20%	16.07%	13.10%	NA
Japonica Intermediate	241	51.00%	29.90%	10.79%	8.30%	NA
VI/Aromatic	96	1.00%	42.70%	46.88%	9.38%	NA
Intermediate	90	20.00%	15.60%	14.44%	50.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0901628621	C -> DEL	N	N	silent_mutation	Average:38.951; most accessible tissue: Zhenshan97 flag leaf, score: 58.772	N	N	N	N
vg0901628621	C -> T	LOC_Os09g03360.1	upstream_gene_variant ; 2248.0bp to feature; MODIFIER	silent_mutation	Average:38.951; most accessible tissue: Zhenshan97 flag leaf, score: 58.772	N	N	N	N
vg0901628621	C -> T	LOC_Os09g03350.1	downstream_gene_variant ; 2484.0bp to feature; MODIFIER	silent_mutation	Average:38.951; most accessible tissue: Zhenshan97 flag leaf, score: 58.772	N	N	N	N
vg0901628621	C -> T	LOC_Os09g03350-LOC_Os09g03360	intergenic_region ; MODIFIER	silent_mutation	Average:38.951; most accessible tissue: Zhenshan97 flag leaf, score: 58.772	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0901628621	NA	1.95E-07	mr1596	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
vg0901628621	3.60E-07	NA	mr1070_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
vg0901628621	2.23E-07	NA	mr1083_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
vg0901628621	5.06E-07	NA	mr1103_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
vg0901628621	9.09E-09	NA	mr1104_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
vg0901628621	3.35E-06	NA	mr1145_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
vg0901628621	1.22E-07	NA	mr1226_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
vg0901628621	NA	2.50E-06	mr1246_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
vg0901628621	9.23E-07	NA	mr1437_2	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
vg0901628621	NA	3.22E-07	mr1554_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
vg0901628621	NA	2.50E-07	mr1578_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