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Detailed information for vg0709483572:

Variant ID: vg0709483572 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 9483572
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GATCGTTATATGCATTGAGGCGTAAGGTGTCAGAAGCAACACTTCGACCTTAGGTTTGGGTTTTGTCGGACTTTACAACCAACGGTTCGACGTCGGGTCA[G/A]
AAGACCGTGCGAACGTCCCCATGGAAGGCGTAAAGTTCCAAACGGTGGTTGTTTAGTGGCAAAGGGTATTTTTGGGTAAAAAGAAAATATTTGAAAGGCA

Reverse complement sequence

TGCCTTTCAAATATTTTCTTTTTACCCAAAAATACCCTTTGCCACTAAACAACCACCGTTTGGAACTTTACGCCTTCCATGGGGACGTTCGCACGGTCTT[C/T]
TGACCCGACGTCGAACCGTTGGTTGTAAAGTCCGACAAAACCCAAACCTAAGGTCGAAGTGTTGCTTCTGACACCTTACGCCTCAATGCATATAACGATC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	88.60%	6.80%	2.50%	2.09%	NA
All Indica	2759	99.50%	0.40%	0.07%	0.00%	NA
All Japonica	1512	75.90%	10.10%	7.47%	6.48%	NA
Aus	269	43.90%	55.80%	0.37%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	99.80%	0.00%	0.22%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	98.50%	1.50%	0.00%	0.00%	NA
Temperate Japonica	767	99.70%	0.00%	0.13%	0.13%	NA
Tropical Japonica	504	31.50%	28.20%	21.43%	18.85%	NA
Japonica Intermediate	241	92.90%	4.60%	1.66%	0.83%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	88.90%	7.80%	2.22%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0709483572	G -> DEL	N	N	silent_mutation	Average:32.995; most accessible tissue: Minghui63 flag leaf, score: 45.195	N	N	N	N
vg0709483572	G -> A	LOC_Os07g16240.1	downstream_gene_variant ; 4646.0bp to feature; MODIFIER	silent_mutation	Average:32.995; most accessible tissue: Minghui63 flag leaf, score: 45.195	N	N	N	N
vg0709483572	G -> A	LOC_Os07g16250.1	downstream_gene_variant ; 2587.0bp to feature; MODIFIER	silent_mutation	Average:32.995; most accessible tissue: Minghui63 flag leaf, score: 45.195	N	N	N	N
vg0709483572	G -> A	LOC_Os07g16240-LOC_Os07g16250	intergenic_region ; MODIFIER	silent_mutation	Average:32.995; most accessible tissue: Minghui63 flag leaf, score: 45.195	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0709483572	NA	8.30E-17	mr1261	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
vg0709483572	NA	4.29E-06	mr1277	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
vg0709483572	NA	3.25E-07	mr1345	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
vg0709483572	NA	7.36E-08	mr1551	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
vg0709483572	NA	9.41E-08	mr1559	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
vg0709483572	NA	7.88E-08	mr1277_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
vg0709483572	NA	4.33E-06	mr1319_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
vg0709483572	1.25E-06	1.25E-06	mr1335_2	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
vg0709483572	NA	2.19E-15	mr1338_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
vg0709483572	NA	8.75E-08	mr1338_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
vg0709483572	NA	9.59E-09	mr1363_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
vg0709483572	NA	3.34E-07	mr1363_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
vg0709483572	NA	4.41E-10	mr1825_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
vg0709483572	NA	3.95E-11	mr1851_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
vg0709483572	NA	3.20E-13	mr1864_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
vg0709483572	NA	6.69E-08	mr1966_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