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Detailed information for vg0101387635:

Variant ID: vg0101387635 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 1387635
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCGAAAGGATCGCTTCGCCAGTTGAGACACTCAAGAAATGGAGCTTCCATTCTCTCTAGATGTGTGGGAAGATGAAAGATGATATGAAGAGCTTGTATTC[G/A]
GCTTGTCTATTATATAGGGCCGCAACTAGTGCTATAACTGGACTTAATTTTGTTCATCTGGCCCACTTGATGTGACAACACGCGCACGCGTGAGCATCAT

Reverse complement sequence

ATGATGCTCACGCGTGCGCGTGTTGTCACATCAAGTGGGCCAGATGAACAAAATTAAGTCCAGTTATAGCACTAGTTGCGGCCCTATATAATAGACAAGC[C/T]
GAATACAAGCTCTTCATATCATCTTTCATCTTCCCACACATCTAGAGAGAATGGAAGCTCCATTTCTTGAGTGTCTCAACTGGCGAAGCGATCCTTTCGC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	84.20%	2.90%	4.72%	8.19%	NA
All Indica	2759	84.30%	4.80%	6.56%	4.31%	NA
All Japonica	1512	80.60%	0.10%	2.18%	17.20%	NA
Aus	269	98.90%	0.70%	0.00%	0.37%	NA
Indica I	595	49.60%	18.00%	22.69%	9.75%	NA
Indica II	465	98.70%	0.00%	0.65%	0.65%	NA
Indica III	913	96.80%	0.20%	1.10%	1.86%	NA
Indica Intermediate	786	87.50%	3.10%	4.20%	5.22%	NA
Temperate Japonica	767	68.10%	0.10%	3.52%	28.29%	NA
Tropical Japonica	504	98.60%	0.00%	0.40%	0.99%	NA
Japonica Intermediate	241	82.60%	0.00%	1.66%	15.77%	NA
VI/Aromatic	96	90.60%	0.00%	4.17%	5.21%	NA
Intermediate	90	90.00%	2.20%	5.56%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0101387635	G -> A	LOC_Os01g03440.1	downstream_gene_variant ; 2551.0bp to feature; MODIFIER	silent_mutation	Average:25.043; most accessible tissue: Minghui63 root, score: 55.188	N	N	N	N
vg0101387635	G -> A	LOC_Os01g03452.1	intron_variant ; MODIFIER	silent_mutation	Average:25.043; most accessible tissue: Minghui63 root, score: 55.188	N	N	N	N
vg0101387635	G -> DEL	N	N	silent_mutation	Average:25.043; most accessible tissue: Minghui63 root, score: 55.188	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0101387635	3.40E-06	3.40E-06	mr1819	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
vg0101387635	NA	8.09E-06	mr1355_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
vg0101387635	NA	5.16E-06	mr1655_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