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Detailed information for vg0711831639:

Variant ID: vg0711831639 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 11831639
Reference Allele: A	Alternative Allele: G,T
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAAAAGTCATGACAACCCACTCAAACAAACCAACAAATCCCGGGCATCTAAAAGCCGTCTTGTACATATCCTCTTCCGCCATAAAGATTTGATTGTAGCC[A/G,T]
GCATTACCATCTAGAAAGCTAATCACCTTATGACCCGAGGCATCATTAATCATCATGTCGGCTATAGGCATAGGATACTTATCTTTGGGAGTGGCTTTAT

Reverse complement sequence

ATAAAGCCACTCCCAAAGATAAGTATCCTATGCCTATAGCCGACATGATGATTAATGATGCCTCGGGTCATAAGGTGATTAGCTTTCTAGATGGTAATGC[T/C,A]
GGCTACAATCAAATCTTTATGGCGGAAGAGGATATGTACAAGACGGCTTTTAGATGCCCGGGATTTGTTGGTTTGTTTGAGTGGGTTGTCATGACTTTTG

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	91.50%	1.00%	0.55%	6.90%	NA
All Indica	2759	98.60%	0.10%	0.36%	0.91%	NA
All Japonica	1512	83.10%	0.10%	0.46%	16.34%	NA
Aus	269	80.70%	15.60%	0.74%	2.97%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.90%	0.00%	0.00%	0.11%	NA
Indica Intermediate	786	95.20%	0.50%	1.27%	3.05%	NA
Temperate Japonica	767	71.80%	0.10%	0.91%	27.12%	NA
Tropical Japonica	504	99.60%	0.00%	0.00%	0.40%	NA
Japonica Intermediate	241	84.60%	0.00%	0.00%	15.35%	NA
VI/Aromatic	96	49.00%	1.00%	6.25%	43.75%	NA
Intermediate	90	93.30%	1.10%	1.11%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0711831639	A -> DEL	LOC_Os07g20490.1	N	frameshift_variant	Average:40.602; most accessible tissue: Zhenshan97 flag leaf, score: 56.722	N	N	N	N
vg0711831639	A -> G	LOC_Os07g20490.1	synonymous_variant ; p.Ala373Ala; LOW	synonymous_codon	Average:40.602; most accessible tissue: Zhenshan97 flag leaf, score: 56.722	N	N	N	N
vg0711831639	A -> T	LOC_Os07g20490.1	synonymous_variant ; p.Ala373Ala; LOW	N	Average:40.602; most accessible tissue: Zhenshan97 flag leaf, score: 56.722	N	N	N	N
vg0711831639	A -> T	LOC_Os07g20480.1	upstream_gene_variant ; 3629.0bp to feature; MODIFIER	N	Average:40.602; most accessible tissue: Zhenshan97 flag leaf, score: 56.722	N	N	N	N
vg0711831639	A -> T	LOC_Os07g20500.1	downstream_gene_variant ; 4969.0bp to feature; MODIFIER	N	Average:40.602; most accessible tissue: Zhenshan97 flag leaf, score: 56.722	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0711831639	7.51E-08	7.51E-08	mr1833	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