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Detailed information for vg0611426472:

Variant ID: vg0611426472 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 11426472
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.83, T: 0.14, others allele: 0.00, population size: 41. )

Flanking Sequence (100 bp) in Reference Genome:

TGCACAGCACACCAGGGTTTAACTCACCGCCGGTAACCGCGCGGTTACCGCGGTTACCGGGCTTACCGCGGGGGTACGGTAATATAAATACCGTGGTAAC[T/C]
TCCTTAAATACAAATAAATTTAAAAAATAATTTGAATTTTTGATAAATTTTGCACGGTTTTGTACGGTTTTTCACGGTTACCGCGGTTACCGAGCGGTAA

Reverse complement sequence

TTACCGCTCGGTAACCGCGGTAACCGTGAAAAACCGTACAAAACCGTGCAAAATTTATCAAAAATTCAAATTATTTTTTAAATTTATTTGTATTTAAGGA[A/G]
GTTACCACGGTATTTATATTACCGTACCCCCGCGGTAAGCCCGGTAACCGCGGTAACCGCGCGGTTACCGGCGGTGAGTTAAACCCTGGTGTGCTGTGCA

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	36.80%	1.30%	0.68%	61.30%	NA
All Indica	2759	4.30%	0.00%	0.72%	95.00%	NA
All Japonica	1512	85.30%	4.00%	0.53%	10.25%	NA
Aus	269	75.10%	0.00%	0.00%	24.91%	NA
Indica I	595	7.20%	0.00%	0.50%	92.27%	NA
Indica II	465	3.00%	0.00%	0.22%	96.77%	NA
Indica III	913	1.30%	0.00%	1.10%	97.59%	NA
Indica Intermediate	786	6.20%	0.00%	0.76%	93.00%	NA
Temperate Japonica	767	90.40%	6.30%	0.13%	3.26%	NA
Tropical Japonica	504	75.40%	0.80%	0.99%	22.82%	NA
Japonica Intermediate	241	89.60%	3.30%	0.83%	6.22%	NA
VI/Aromatic	96	85.40%	0.00%	1.04%	13.54%	NA
Intermediate	90	51.10%	0.00%	3.33%	45.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0611426472	T -> C	LOC_Os06g19940.1	upstream_gene_variant ; 4088.0bp to feature; MODIFIER	silent_mutation	Average:58.846; most accessible tissue: Minghui63 root, score: 78.833	N	N	N	N
vg0611426472	T -> C	LOC_Os06g19950.1	downstream_gene_variant ; 1537.0bp to feature; MODIFIER	silent_mutation	Average:58.846; most accessible tissue: Minghui63 root, score: 78.833	N	N	N	N
vg0611426472	T -> C	LOC_Os06g19950-LOC_Os06g19960	intergenic_region ; MODIFIER	silent_mutation	Average:58.846; most accessible tissue: Minghui63 root, score: 78.833	N	N	N	N
vg0611426472	T -> DEL	N	N	silent_mutation	Average:58.846; most accessible tissue: Minghui63 root, score: 78.833	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0611426472	NA	3.39E-06	mr1121	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
vg0611426472	NA	3.20E-42	mr1144	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
vg0611426472	NA	1.99E-09	mr1151	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
vg0611426472	NA	7.98E-42	mr1200	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
vg0611426472	9.59E-06	4.24E-06	mr1200	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
vg0611426472	NA	4.18E-08	mr1249	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
vg0611426472	NA	2.94E-06	mr1990	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
vg0611426472	NA	4.04E-09	mr1068_2	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
vg0611426472	6.10E-06	1.97E-10	mr1087_2	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
vg0611426472	NA	2.91E-08	mr1111_2	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
vg0611426472	NA	3.42E-09	mr1112_2	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
vg0611426472	NA	3.18E-06	mr1121_2	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
vg0611426472	2.06E-06	8.16E-11	mr1200_2	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
vg0611426472	NA	5.25E-07	mr1211_2	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
vg0611426472	NA	8.76E-08	mr1399_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