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Detailed information for vg0113613619:

Variant ID: vg0113613619 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 13613619
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GACCCCGTCAGCCTGGTATTGATATTGACGTATTTCTTGAACCATTGTTGGAAGATATGGCTGATTTATGGAAAGAGGGATTGAAAATGTGGGACGAGTA[C/T]
TTAAGAGAATACTTCACAGTGAAGGCCATCATCTTCGTGACCATTAACGATTATCCAGCAATGTTTTCAGTTTCAGGTCAAATTAAAGGTAAAAACAGGA

Reverse complement sequence

TCCTGTTTTTACCTTTAATTTGACCTGAAACTGAAAACATTGCTGGATAATCGTTAATGGTCACGAAGATGATGGCCTTCACTGTGAAGTATTCTCTTAA[G/A]
TACTCGTCCCACATTTTCAATCCCTCTTTCCATAAATCAGCCATATCTTCCAACAATGGTTCAAGAAATACGTCAATATCAATACCAGGCTGACGGGGTC

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	54.00%	0.80%	7.70%	37.54%	NA
All Indica	2759	39.20%	0.70%	9.53%	50.63%	NA
All Japonica	1512	87.50%	0.20%	2.58%	9.72%	NA
Aus	269	20.80%	0.40%	13.38%	65.43%	NA
Indica I	595	58.80%	0.30%	3.19%	37.65%	NA
Indica II	465	26.90%	0.00%	7.31%	65.81%	NA
Indica III	913	33.10%	1.50%	14.57%	50.82%	NA
Indica Intermediate	786	38.70%	0.30%	9.80%	51.27%	NA
Temperate Japonica	767	98.80%	0.00%	0.26%	0.91%	NA
Tropical Japonica	504	67.50%	0.60%	6.75%	25.20%	NA
Japonica Intermediate	241	93.40%	0.00%	1.24%	5.39%	NA
VI/Aromatic	96	39.60%	15.60%	20.83%	23.96%	NA
Intermediate	90	57.80%	1.10%	6.67%	34.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0113613619	C -> T	LOC_Os01g24140.1	synonymous_variant ; p.Tyr377Tyr; LOW	synonymous_codon	Average:21.738; most accessible tissue: Zhenshan97 root, score: 53.045	N	N	N	N
vg0113613619	C -> DEL	LOC_Os01g24140.1	N	frameshift_variant	Average:21.738; most accessible tissue: Zhenshan97 root, score: 53.045	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0113613619	1.15E-07	NA	mr1168	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
vg0113613619	9.43E-10	NA	mr1383	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
vg0113613619	1.05E-07	2.04E-06	mr1383	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