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Detailed information for vg0113970354:

Variant ID: vg0113970354 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 13970354
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTTTGTTTCTTGTACTAGAGGGTTTCCTAAGGTGTTTAGGACTCCTAGTATGAGTTTGGTTCGTGGTTTTAGGTTGCCTATCTCATGTATAAATAGAGGG[T/G]
GAGCGTGAGGCTTCCCGGTATCGCTTTTGAGAGCAATTGAGTTGAGTTTTAAGTTAGGGTTTCGAGTTTAGTCAAAATTTTTGTAAGGAGTGCTGTTGGT

Reverse complement sequence

ACCAACAGCACTCCTTACAAAAATTTTGACTAAACTCGAAACCCTAACTTAAAACTCAACTCAATTGCTCTCAAAAGCGATACCGGGAAGCCTCACGCTC[A/C]
CCCTCTATTTATACATGAGATAGGCAACCTAAAACCACGAACCAAACTCATACTAGGAGTCCTAAACACCTTAGGAAACCCTCTAGTACAAGAAACAAAC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	95.30%	0.10%	3.32%	1.29%	NA
All Indica	2759	93.50%	0.10%	4.35%	2.07%	NA
All Japonica	1512	97.30%	0.10%	2.38%	0.26%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	87.70%	0.00%	7.90%	4.37%	NA
Indica II	465	97.60%	0.20%	1.51%	0.65%	NA
Indica III	913	96.70%	0.10%	2.85%	0.33%	NA
Indica Intermediate	786	91.70%	0.00%	5.09%	3.18%	NA
Temperate Japonica	767	98.30%	0.00%	1.56%	0.13%	NA
Tropical Japonica	504	95.00%	0.20%	4.17%	0.60%	NA
Japonica Intermediate	241	98.80%	0.00%	1.24%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	2.20%	1.11%	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
vg0113970354	T -> G	LOC_Os01g24800.1	downstream_gene_variant ; 224.0bp to feature; MODIFIER	silent_mutation	Average:31.128; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg0113970354	T -> G	LOC_Os01g24800-LOC_Os01g24810	intergenic_region ; MODIFIER	silent_mutation	Average:31.128; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg0113970354	T -> DEL	N	N	silent_mutation	Average:31.128; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0113970354	NA	8.30E-06	mr1064	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
vg0113970354	NA	4.44E-07	mr1125	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
vg0113970354	3.14E-06	1.16E-07	mr1448	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
vg0113970354	NA	1.17E-07	mr1458	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
vg0113970354	4.52E-06	1.75E-06	mr1541	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
vg0113970354	NA	2.60E-06	mr1631	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
vg0113970354	4.97E-06	7.90E-06	mr1654	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