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Detailed information for vg0400871651:

Variant ID: vg0400871651 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 871651
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATAGGGCGCCTATCGAACGGTCAGAGCGCGACTGGCGAGGAGATCGGAAGGCTGCCGTTCGACAGGACCTGTCGAACAGCCCCCGTTCGACAGGCAGGGC[T/A]
GTCGAACTGCCCCTGTTCGACAGGATATCCGTCGAACTGGCACAGTTCGACAGGGTCGCGTTCTCCATTTATTTGTAATAAGTTATTTTTTTTAATAATT

Reverse complement sequence

AATTATTAAAAAAAATAACTTATTACAAATAAATGGAGAACGCGACCCTGTCGAACTGTGCCAGTTCGACGGATATCCTGTCGAACAGGGGCAGTTCGAC[A/T]
GCCCTGCCTGTCGAACGGGGGCTGTTCGACAGGTCCTGTCGAACGGCAGCCTTCCGATCTCCTCGCCAGTCGCGCTCTGACCGTTCGATAGGCGCCCTAT

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	63.00%	1.70%	7.05%	28.31%	NA
All Indica	2759	72.10%	0.70%	2.54%	24.68%	NA
All Japonica	1512	44.40%	1.50%	12.83%	41.34%	NA
Aus	269	71.70%	10.00%	18.22%	0.00%	NA
Indica I	595	34.50%	0.20%	4.03%	61.34%	NA
Indica II	465	83.70%	0.20%	1.08%	15.05%	NA
Indica III	913	86.30%	1.50%	1.86%	10.30%	NA
Indica Intermediate	786	77.10%	0.50%	3.05%	19.34%	NA
Temperate Japonica	767	63.80%	1.30%	17.21%	17.73%	NA
Tropical Japonica	504	23.20%	0.60%	6.55%	69.64%	NA
Japonica Intermediate	241	27.00%	3.70%	12.03%	57.26%	NA
VI/Aromatic	96	58.30%	10.40%	15.62%	15.62%	NA
Intermediate	90	75.60%	0.00%	5.56%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0400871651	T -> DEL	N	N	silent_mutation	Average:37.555; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N
vg0400871651	T -> A	LOC_Os04g02410.1	upstream_gene_variant ; 2872.0bp to feature; MODIFIER	silent_mutation	Average:37.555; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N
vg0400871651	T -> A	LOC_Os04g02420.1	downstream_gene_variant ; 411.0bp to feature; MODIFIER	silent_mutation	Average:37.555; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N
vg0400871651	T -> A	LOC_Os04g02410-LOC_Os04g02420	intergenic_region ; MODIFIER	silent_mutation	Average:37.555; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0400871651	7.39E-12	7.39E-12	mr1343	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
vg0400871651	NA	3.27E-06	mr1354	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
vg0400871651	1.66E-06	2.49E-07	mr1415	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
vg0400871651	NA	3.34E-06	mr1548	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
vg0400871651	1.66E-06	2.49E-07	mr1567	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
vg0400871651	2.65E-07	2.69E-11	mr1829	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
vg0400871651	1.44E-06	1.44E-06	mr1842	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
vg0400871651	NA	5.35E-07	mr1902	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
vg0400871651	NA	2.31E-06	mr1829_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