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Detailed information for vg0136242530:

Variant ID: vg0136242530 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 36242530
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTGAGATTTTAAAAATTAAACATATTTATCGTTTGGGTTCATTTTTACTTTCTAGAAGTCCCGCCAAACCGTCAGCGGCTTTGCCATTGTACTCCTCTA[C/T]
GGCTCACCCACTGCCTCCCTTCTTTATTGTCATTGAGATTTTAAAATCGAACATGATTATCATTGCTTTTTTTTTACTTTTTGGAAGTTCCGAACCTTTA

Reverse complement sequence

TAAAGGTTCGGAACTTCCAAAAAGTAAAAAAAAAGCAATGATAATCATGTTCGATTTTAAAATCTCAATGACAATAAAGAAGGGAGGCAGTGGGTGAGCC[G/A]
TAGAGGAGTACAATGGCAAAGCCGCTGACGGTTTGGCGGGACTTCTAGAAAGTAAAAATGAACCCAAACGATAAATATGTTTAATTTTTAAAATCTCAAT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	98.00%	2.00%	0.00%	0.00%	NA
All Indica	2759	96.70%	3.30%	0.00%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	90.40%	9.60%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	98.80%	1.20%	0.00%	0.00%	NA
Indica Intermediate	786	96.90%	3.10%	0.00%	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	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	3.30%	0.00%	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
vg0136242530	C -> T	LOC_Os01g62600.1	downstream_gene_variant ; 3464.0bp to feature; MODIFIER	silent_mutation	Average:28.365; most accessible tissue: Minghui63 panicle, score: 66.554	N	N	N	N
vg0136242530	C -> T	LOC_Os01g62600-LOC_Os01g62605	intergenic_region ; MODIFIER	silent_mutation	Average:28.365; most accessible tissue: Minghui63 panicle, score: 66.554	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0136242530	NA	3.96E-07	mr1060	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
vg0136242530	1.21E-06	4.93E-08	mr1621	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