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Detailed information for vg1104173599:

Variant ID: vg1104173599 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 4173599
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTTACGCGCGACTTATCCGGTTCGGTTACGCGCAGTAGAGATCGTGCGGGCGCCCTGATCAAGCGACCCTTCTCTATATAAACCGACCTGCCGTCTTCAC[G/A]
CAACACTTGCGAAATCAATCTAGGGTTTGCCTCCTACTCTGTACTGCGCCGTCGCTCGTAGACTACTCCATCCCGCTCGCCGGCGTGCACCGGCGATCGG

Reverse complement sequence

CCGATCGCCGGTGCACGCCGGCGAGCGGGATGGAGTAGTCTACGAGCGACGGCGCAGTACAGAGTAGGAGGCAAACCCTAGATTGATTTCGCAAGTGTTG[C/T]
GTGAAGACGGCAGGTCGGTTTATATAGAGAAGGGTCGCTTGATCAGGGCGCCCGCACGATCTCTACTGCGCGTAACCGAACCGGATAAGTCGCGCGTAAC

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	82.10%	0.70%	4.23%	12.95%	NA
All Indica	2759	79.50%	1.20%	5.94%	13.34%	NA
All Japonica	1512	83.70%	0.10%	1.79%	14.42%	NA
Aus	269	91.80%	0.00%	2.23%	5.95%	NA
Indica I	595	86.40%	0.70%	4.87%	8.07%	NA
Indica II	465	70.10%	0.20%	8.60%	21.08%	NA
Indica III	913	82.50%	1.50%	5.04%	10.95%	NA
Indica Intermediate	786	76.50%	1.80%	6.23%	15.52%	NA
Temperate Japonica	767	97.80%	0.00%	0.00%	2.22%	NA
Tropical Japonica	504	59.50%	0.40%	4.96%	35.12%	NA
Japonica Intermediate	241	89.20%	0.00%	0.83%	9.96%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	86.70%	0.00%	2.22%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1104173599	G -> A	LOC_Os11g08020.1	intron_variant ; MODIFIER	silent_mutation	Average:17.438; most accessible tissue: Minghui63 root, score: 46.493	N	N	N	N
vg1104173599	G -> DEL	N	N	silent_mutation	Average:17.438; most accessible tissue: Minghui63 root, score: 46.493	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1104173599	NA	3.35E-07	mr1408	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
vg1104173599	8.44E-06	NA	mr1845	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
vg1104173599	3.99E-06	3.99E-06	mr1845	Ind_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