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Detailed information for vg0107608673:

Variant ID: vg0107608673 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 7608673
Reference Allele: A	Alternative Allele: T
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTTGTACCGGGAAGCAATCTTGACCGGACACTCAACCCCGATTCACTCAAATATACTCCCTTTCGTTTGAAAAAAAAAAGAATCAGGGCTGAATGTAACA[A/T]
ATTTTAGTAAAAAAACTCTAAACGAATGCATGTCCAGATTTATAGTTCTAGAATGTATCACATCGAGTATTAAGGGAGAACAAAATACCATAATGTGCAT

Reverse complement sequence

ATGCACATTATGGTATTTTGTTCTCCCTTAATACTCGATGTGATACATTCTAGAACTATAAATCTGGACATGCATTCGTTTAGAGTTTTTTTACTAAAAT[T/A]
TGTTACATTCAGCCCTGATTCTTTTTTTTTTCAAACGAAAGGGAGTATATTTGAGTGAATCGGGGTTGAGTGTCCGGTCAAGATTGCTTCCCGGTACAAC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	67.10%	32.80%	0.11%	0.00%	NA
All Indica	2759	99.20%	0.80%	0.07%	0.00%	NA
All Japonica	1512	6.70%	93.30%	0.07%	0.00%	NA
Aus	269	97.80%	2.20%	0.00%	0.00%	NA
Indica I	595	99.50%	0.50%	0.00%	0.00%	NA
Indica II	465	99.10%	0.90%	0.00%	0.00%	NA
Indica III	913	99.70%	0.30%	0.00%	0.00%	NA
Indica Intermediate	786	98.30%	1.40%	0.25%	0.00%	NA
Temperate Japonica	767	7.60%	92.30%	0.13%	0.00%	NA
Tropical Japonica	504	5.20%	94.80%	0.00%	0.00%	NA
Japonica Intermediate	241	7.10%	92.90%	0.00%	0.00%	NA
VI/Aromatic	96	19.80%	80.20%	0.00%	0.00%	NA
Intermediate	90	58.90%	38.90%	2.22%	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
vg0107608673	A -> T	LOC_Os01g13600.1	upstream_gene_variant ; 2128.0bp to feature; MODIFIER	silent_mutation	Average:42.772; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg0107608673	A -> T	LOC_Os01g13600-LOC_Os01g13610	intergenic_region ; MODIFIER	silent_mutation	Average:42.772; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0107608673	NA	2.78E-80	mr1134	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
vg0107608673	NA	7.89E-78	mr1135	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
vg0107608673	NA	3.67E-27	mr1309	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
vg0107608673	NA	5.95E-23	mr1375	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
vg0107608673	NA	1.46E-88	mr1504	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
vg0107608673	NA	2.64E-86	mr1517	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
vg0107608673	NA	2.54E-69	mr1538	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
vg0107608673	NA	1.22E-81	mr1672	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
vg0107608673	NA	3.77E-16	mr1416_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
vg0107608673	NA	1.86E-85	mr1504_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
vg0107608673	2.22E-07	NA	mr1517_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
vg0107608673	NA	7.00E-06	mr1517_2	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
vg0107608673	5.52E-08	2.85E-108	mr1538_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
vg0107608673	NA	1.68E-36	mr1541_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