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Detailed information for vg0324719195:

Variant ID: vg0324719195 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 24719195
Reference Allele: A	Alternative Allele: T,C
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGGGTTCGGGTTGCTACAGTGTCTTGAGGGGGGGTATAGGCAATATTTGTGAAATGCTGTAATGCGGAGAGGGCCGAGTGCAAAAGTGTTGCCTACGTGG[A/T,C]
GCGCTAGGTTGGCAGTTAATCGCAGTAGTCAAAGGGCTATTGAACCGGGGCATGGTACATTAAACCAAGTTGACCTAAACGTGATTTTCAAGTTTACGGA

Reverse complement sequence

TCCGTAAACTTGAAAATCACGTTTAGGTCAACTTGGTTTAATGTACCATGCCCCGGTTCAATAGCCCTTTGACTACTGCGATTAACTGCCAACCTAGCGC[T/A,G]
CCACGTAGGCAACACTTTTGCACTCGGCCCTCTCCGCATTACAGCATTTCACAAATATTGCCTATACCCCCCCTCAAGACACTGTAGCAACCCGAACCCA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	89.20%	10.70%	0.11%	0.00%	C: 0.04%
All Indica	2759	90.20%	9.60%	0.18%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	17.10%	82.90%	0.00%	0.00%	NA
Indica I	595	85.00%	14.60%	0.34%	0.00%	NA
Indica II	465	97.80%	2.20%	0.00%	0.00%	NA
Indica III	913	89.20%	10.80%	0.00%	0.00%	NA
Indica Intermediate	786	90.80%	8.80%	0.38%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	85.60%	12.20%	0.00%	0.00%	C: 2.22%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0324719195	A -> T	LOC_Os03g44000.1	upstream_gene_variant ; 2033.0bp to feature; MODIFIER	silent_mutation	Average:60.071; most accessible tissue: Zhenshan97 root, score: 78.63	N	N	N	N
vg0324719195	A -> T	LOC_Os03g43990-LOC_Os03g44000	intergenic_region ; MODIFIER	silent_mutation	Average:60.071; most accessible tissue: Zhenshan97 root, score: 78.63	N	N	N	N
vg0324719195	A -> C	LOC_Os03g44000.1	upstream_gene_variant ; 2033.0bp to feature; MODIFIER	silent_mutation	Average:60.071; most accessible tissue: Zhenshan97 root, score: 78.63	N	N	N	N
vg0324719195	A -> C	LOC_Os03g43990-LOC_Os03g44000	intergenic_region ; MODIFIER	silent_mutation	Average:60.071; most accessible tissue: Zhenshan97 root, score: 78.63	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0324719195	NA	2.85E-06	mr1207	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
vg0324719195	NA	4.10E-06	mr1522_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
vg0324719195	1.15E-06	1.15E-06	mr1634_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