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Detailed information for vg0406818237:

Variant ID: vg0406818237 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 6818237
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTACCTTGTACTTTTGCACCATTGTCCCCTTGCGGGTCTGCATAAATGAGTTTAAGAACTGGTTCCGTGCTTGCTGCATCATCGCTTCAAAATCTTTCTT[T/C]
TGATCGGGTGTCAGCTTGTCTGGAGTAATGTTCACGATGTTGCCTTCATTAACCTCGTATTGGTCTAACTGCTGGATCTTCACTTTAACAGAACCTGGGC

Reverse complement sequence

GCCCAGGTTCTGTTAAAGTGAAGATCCAGCAGTTAGACCAATACGAGGTTAATGAAGGCAACATCGTGAACATTACTCCAGACAAGCTGACACCCGATCA[A/G]
AAGAAAGATTTTGAAGCGATGATGCAGCAAGCACGGAACCAGTTCTTAAACTCATTTATGCAGACCCGCAAGGGGACAATGGTGCAAAAGTACAAGGTAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	55.10%	0.30%	7.53%	37.05%	NA
All Indica	2759	36.40%	0.50%	10.87%	52.19%	NA
All Japonica	1512	98.10%	0.00%	0.07%	1.85%	NA
Aus	269	10.80%	0.00%	14.13%	75.09%	NA
Indica I	595	40.30%	0.20%	11.26%	48.24%	NA
Indica II	465	35.90%	0.90%	7.53%	55.70%	NA
Indica III	913	32.00%	0.40%	13.36%	54.22%	NA
Indica Intermediate	786	38.80%	0.80%	9.67%	50.76%	NA
Temperate Japonica	767	99.90%	0.00%	0.00%	0.13%	NA
Tropical Japonica	504	96.80%	0.00%	0.20%	2.98%	NA
Japonica Intermediate	241	95.00%	0.00%	0.00%	4.98%	NA
VI/Aromatic	96	27.10%	0.00%	15.62%	57.29%	NA
Intermediate	90	67.80%	1.10%	2.22%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0406818237	T -> C	LOC_Os04g12360.1	synonymous_variant ; p.Gln46Gln; LOW	synonymous_codon	Average:43.951; most accessible tissue: Minghui63 young leaf, score: 78.443	N	N	N	N
vg0406818237	T -> DEL	LOC_Os04g12360.1	N	frameshift_variant	Average:43.951; most accessible tissue: Minghui63 young leaf, score: 78.443	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0406818237	NA	1.64E-06	mr1015	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
vg0406818237	NA	4.14E-13	mr1035	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
vg0406818237	NA	1.17E-06	mr1305	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
vg0406818237	NA	1.50E-06	mr1409	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
vg0406818237	NA	9.53E-06	mr1515	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
vg0406818237	NA	3.16E-12	mr1626	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
vg0406818237	NA	4.27E-06	mr1649	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
vg0406818237	1.95E-06	1.95E-06	mr1687	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
vg0406818237	NA	3.85E-06	mr1895	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
vg0406818237	NA	3.39E-07	mr1915	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
vg0406818237	5.17E-07	5.16E-07	mr1966	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
vg0406818237	4.02E-06	4.02E-06	mr1972	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
vg0406818237	NA	5.82E-18	mr1239_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
vg0406818237	NA	1.56E-16	mr1715_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