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Detailed information for vg0611842145:

Variant ID: vg0611842145 (JBrowse)	Variation Type: INDEL
Chromosome: chr06	Position: 11842145
Reference Allele: C	Alternative Allele: T,CTGTCAACGAGCCGAGCTCGAGCG
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.88, C: 0.12, others allele: 0.00, population size: 112. )

Flanking Sequence (100 bp) in Reference Genome:

CCGCATCATGGATCGGTTTCAGAATTAATTCTTATATATATATTTACGACGGTATGTAGAAATTAAACTTCAGAGTCAACATGAAAGCACCAAGTGAAAC[C/T,CTGTCAACGAGCCGAGCTCGAGCG]
AGCTTCCTCCGATTTTTAACCCATCATACCGTTAACTTACGGGTACACATTTGATCATTTTATCTTTTTAAAAAATTTTGTGCTAAACACTTAAGATATA

Reverse complement sequence

TATATCTTAAGTGTTTAGCACAAAATTTTTTAAAAAGATAAAATGATCAAATGTGTACCCGTAAGTTAACGGTATGATGGGTTAAAAATCGGAGGAAGCT[G/A,CGCTCGAGCTCGGCTCGTTGACAG]
GTTTCACTTGGTGCTTTCATGTTGACTCTGAAGTTTAATTTCTACATACCGTCGTAAATATATATATAAGAATTAATTCTGAAACCGATCCATGATGCGG

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	54.40%	45.40%	0.15%	0.00%	NA
All Indica	2759	75.20%	24.50%	0.25%	0.00%	NA
All Japonica	1512	9.20%	90.80%	0.00%	0.00%	NA
Aus	269	92.20%	7.80%	0.00%	0.00%	NA
Indica I	595	96.00%	3.70%	0.34%	0.00%	NA
Indica II	465	84.70%	15.10%	0.22%	0.00%	NA
Indica III	913	55.90%	43.90%	0.22%	0.00%	NA
Indica Intermediate	786	76.30%	23.40%	0.25%	0.00%	NA
Temperate Japonica	767	1.80%	98.20%	0.00%	0.00%	NA
Tropical Japonica	504	20.20%	79.80%	0.00%	0.00%	NA
Japonica Intermediate	241	9.50%	90.50%	0.00%	0.00%	NA
VI/Aromatic	96	69.80%	30.20%	0.00%	0.00%	NA
Intermediate	90	48.90%	51.10%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0611842145	C -> T	LOC_Os06g20560.1	upstream_gene_variant ; 3865.0bp to feature; MODIFIER	silent_mutation	Average:40.624; most accessible tissue: Zhenshan97 root, score: 63.237	N	N	N	N
vg0611842145	C -> T	LOC_Os06g20580.1	upstream_gene_variant ; 4567.0bp to feature; MODIFIER	silent_mutation	Average:40.624; most accessible tissue: Zhenshan97 root, score: 63.237	N	N	N	N
vg0611842145	C -> T	LOC_Os06g20570.1	intron_variant ; MODIFIER	silent_mutation	Average:40.624; most accessible tissue: Zhenshan97 root, score: 63.237	N	N	N	N
vg0611842145	C -> CTGTCAACGAGCCGAGCTCGAGCG	LOC_Os06g20560.1	upstream_gene_variant ; 3866.0bp to feature; MODIFIER	N	Average:40.624; most accessible tissue: Zhenshan97 root, score: 63.237	N	N	N	N
vg0611842145	C -> CTGTCAACGAGCCGAGCTCGAGCG	LOC_Os06g20580.1	upstream_gene_variant ; 4566.0bp to feature; MODIFIER	N	Average:40.624; most accessible tissue: Zhenshan97 root, score: 63.237	N	N	N	N
vg0611842145	C -> CTGTCAACGAGCCGAGCTCGAGCG	LOC_Os06g20570.1	intron_variant ; MODIFIER	N	Average:40.624; most accessible tissue: Zhenshan97 root, score: 63.237	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0611842145	NA	1.98E-06	mr1124	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
vg0611842145	NA	2.99E-06	mr1242	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
vg0611842145	NA	3.00E-06	mr1004_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
vg0611842145	NA	9.05E-07	mr1212_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
vg0611842145	NA	2.15E-12	mr1216_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
vg0611842145	NA	1.58E-06	mr1242_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
vg0611842145	NA	3.54E-16	mr1333_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
vg0611842145	NA	3.54E-16	mr1686_2	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
vg0611842145	NA	1.22E-07	mr1795_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