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Detailed information for vg0103394422:

Variant ID: vg0103394422 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 3394422
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 124. )

Flanking Sequence (100 bp) in Reference Genome:

TTTAATTTTAATGCCATATAAGCGCCACGTCAATGCCGCATGAGACAAAGACCCAATCAACAGCGTCATGTCAGTGAAATCATCCTCCAAAACCACTAAG[G/T]
GAGTCAAATTACACTGGTTTCATTAGTTCGGGGAGTCATTTTATCCGGTTTTCTAGTTAAGGGGCATGAATTAGATTTGACCGACTTTTAAGGGAGTCGA

Reverse complement sequence

TCGACTCCCTTAAAAGTCGGTCAAATCTAATTCATGCCCCTTAACTAGAAAACCGGATAAAATGACTCCCCGAACTAATGAAACCAGTGTAATTTGACTC[C/A]
CTTAGTGGTTTTGGAGGATGATTTCACTGACATGACGCTGTTGATTGGGTCTTTGTCTCATGCGGCATTGACGTGGCGCTTATATGGCATTAAAATTAAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	81.80%	8.90%	7.11%	2.24%	NA
All Indica	2759	83.00%	7.60%	7.14%	2.25%	NA
All Japonica	1512	75.00%	13.60%	8.86%	2.58%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	44.70%	22.70%	25.71%	6.89%	NA
Indica II	465	93.30%	3.00%	2.37%	1.29%	NA
Indica III	913	99.20%	0.40%	0.00%	0.33%	NA
Indica Intermediate	786	86.90%	7.40%	4.20%	1.53%	NA
Temperate Japonica	767	96.20%	0.70%	2.74%	0.39%	NA
Tropical Japonica	504	36.30%	37.90%	19.25%	6.55%	NA
Japonica Intermediate	241	88.40%	3.70%	6.64%	1.24%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	84.40%	4.40%	5.56%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0103394422	G -> T	LOC_Os01g07170.1	upstream_gene_variant ; 3666.0bp to feature; MODIFIER	silent_mutation	Average:58.905; most accessible tissue: Zhenshan97 panicle, score: 78.302	N	N	N	N
vg0103394422	G -> T	LOC_Os01g07180.1	upstream_gene_variant ; 1411.0bp to feature; MODIFIER	silent_mutation	Average:58.905; most accessible tissue: Zhenshan97 panicle, score: 78.302	N	N	N	N
vg0103394422	G -> T	LOC_Os01g07190.1	upstream_gene_variant ; 1340.0bp to feature; MODIFIER	silent_mutation	Average:58.905; most accessible tissue: Zhenshan97 panicle, score: 78.302	N	N	N	N
vg0103394422	G -> T	LOC_Os01g07200.1	upstream_gene_variant ; 2915.0bp to feature; MODIFIER	silent_mutation	Average:58.905; most accessible tissue: Zhenshan97 panicle, score: 78.302	N	N	N	N
vg0103394422	G -> T	LOC_Os01g07180-LOC_Os01g07190	intergenic_region ; MODIFIER	silent_mutation	Average:58.905; most accessible tissue: Zhenshan97 panicle, score: 78.302	N	N	N	N
vg0103394422	G -> DEL	N	N	silent_mutation	Average:58.905; most accessible tissue: Zhenshan97 panicle, score: 78.302	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0103394422	NA	1.22E-12	Heading_date	Ind_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0103394422	NA	2.62E-06	mr1092	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
vg0103394422	NA	2.91E-06	mr1097	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
vg0103394422	NA	2.54E-09	mr1539	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
vg0103394422	NA	6.27E-13	mr1539	Jap_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
vg0103394422	NA	2.01E-06	mr1676	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
vg0103394422	NA	2.23E-20	mr1699	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
vg0103394422	NA	1.02E-07	mr1676_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