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Detailed information for vg0123776566:

Variant ID: vg0123776566 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 23776566
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTGCATTGCGTAGCGTGGACTATCACTAACACACAATGGCTAGAATGGCTAGAACTCCAGTTCATCCACGATCGTCCTCGATTGTAGCTGCATTCACTT[A/G]
CCTTTTGCTAGTCCTCTTCCGAGACGCCATCACCACCGCAGCTGCATCTCCCAAAGCTCCGGCATCCACCAATGGCTGCATTGCAGCCGAGAGGGATGCC

Reverse complement sequence

GGCATCCCTCTCGGCTGCAATGCAGCCATTGGTGGATGCCGGAGCTTTGGGAGATGCAGCTGCGGTGGTGATGGCGTCTCGGAAGAGGACTAGCAAAAGG[T/C]
AAGTGAATGCAGCTACAATCGAGGACGATCGTGGATGAACTGGAGTTCTAGCCATTCTAGCCATTGTGTGTTAGTGATAGTCCACGCTACGCAATGCAAT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	43.60%	0.10%	0.17%	56.20%	NA
All Indica	2759	9.90%	0.00%	0.22%	89.85%	NA
All Japonica	1512	92.10%	0.00%	0.00%	7.94%	NA
Aus	269	92.20%	0.00%	0.00%	7.81%	NA
Indica I	595	2.70%	0.00%	0.50%	96.81%	NA
Indica II	465	6.00%	0.00%	0.00%	93.98%	NA
Indica III	913	11.30%	0.00%	0.11%	88.61%	NA
Indica Intermediate	786	16.00%	0.10%	0.25%	83.59%	NA
Temperate Japonica	767	99.50%	0.00%	0.00%	0.52%	NA
Tropical Japonica	504	79.00%	0.00%	0.00%	21.03%	NA
Japonica Intermediate	241	95.90%	0.00%	0.00%	4.15%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	56.70%	2.20%	2.22%	38.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0123776566	A -> G	LOC_Os01g41930.1	missense_variant ; p.Tyr22Cys; MODERATE	nonsynonymous_codon ; Y22C	Average:71.035; most accessible tissue: Minghui63 root, score: 86.253	unknown	unknown	TOLERATED	0.21
vg0123776566	A -> DEL	LOC_Os01g41930.1	N	frameshift_variant	Average:71.035; most accessible tissue: Minghui63 root, score: 86.253	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0123776566	NA	6.90E-19	mr1422	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
vg0123776566	NA	3.04E-07	mr1850	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
vg0123776566	NA	1.89E-06	mr1870_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