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Detailed information for vg0605351193:

Variant ID: vg0605351193 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 5351193
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACAAGTTACTAAAAAAACTAGAATATTAGGGAAGGACCTAATATCAAATAATTAGGAGGGGTGAGGCTTTGAACCCAGGTCGTCTAGCCCACCACCTTGT[G/A]
GAGCTAGCCGGAAGACTCCTAGGCATTTCTCATCTTCCACAAGTTACTCATATCAGCTAAATGAAGTTTTAATACAAACACATGCTAAACATTGTTGTTT

Reverse complement sequence

AAACAACAATGTTTAGCATGTGTTTGTATTAAAACTTCATTTAGCTGATATGAGTAACTTGTGGAAGATGAGAAATGCCTAGGAGTCTTCCGGCTAGCTC[C/T]
ACAAGGTGGTGGGCTAGACGACCTGGGTTCAAAGCCTCACCCCTCCTAATTATTTGATATTAGGTCCTTCCCTAATATTCTAGTTTTTTTAGTAACTTGT

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	85.20%	1.80%	0.49%	12.55%	NA
All Indica	2759	79.60%	0.00%	0.25%	20.08%	NA
All Japonica	1512	94.10%	5.00%	0.79%	0.07%	NA
Aus	269	88.10%	0.00%	0.00%	11.90%	NA
Indica I	595	66.40%	0.00%	0.17%	33.45%	NA
Indica II	465	99.40%	0.20%	0.00%	0.43%	NA
Indica III	913	74.80%	0.00%	0.33%	24.86%	NA
Indica Intermediate	786	83.60%	0.00%	0.38%	16.03%	NA
Temperate Japonica	767	89.40%	9.60%	0.91%	0.00%	NA
Tropical Japonica	504	99.20%	0.00%	0.60%	0.20%	NA
Japonica Intermediate	241	98.30%	0.80%	0.83%	0.00%	NA
VI/Aromatic	96	96.90%	0.00%	3.12%	0.00%	NA
Intermediate	90	85.60%	6.70%	1.11%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0605351193	G -> A	LOC_Os06g10410.1	upstream_gene_variant ; 2514.0bp to feature; MODIFIER	silent_mutation	Average:28.104; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N
vg0605351193	G -> A	LOC_Os06g10410-LOC_Os06g10420	intergenic_region ; MODIFIER	silent_mutation	Average:28.104; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N
vg0605351193	G -> DEL	N	N	silent_mutation	Average:28.104; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0605351193	5.38E-06	5.38E-06	mr1060	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
vg0605351193	NA	1.24E-06	mr1072	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
vg0605351193	8.41E-06	8.41E-06	mr1283	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
vg0605351193	6.06E-06	6.06E-06	mr1288	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
vg0605351193	2.27E-07	2.56E-07	mr1318	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
vg0605351193	NA	4.47E-06	mr1330	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
vg0605351193	NA	7.49E-06	mr1482	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
vg0605351193	3.62E-06	NA	mr1707	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
vg0605351193	NA	1.77E-06	mr1763	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
vg0605351193	NA	2.93E-06	mr1775	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
vg0605351193	NA	4.87E-06	mr1829	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