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Detailed information for vg0423691960:

Variant ID: vg0423691960 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 23691960
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAGTCTAAGGCTATATTACACTTTTCCCTAAGATGACAATCGCAGGATACAAAGACTACCAAGAAGGCCAACGCCAGTCCATAGATTGTAAGACCTTCTC[C/T]
GCCAACGACACCATCGACTTCGCCAGGTGGTCTATCTCCGCCGGAGTCCTCCGAGAACGAGCAAAACCTTCACGGAGAAAATCGAGGTCCAGTCGCGGGC

Reverse complement sequence

GCCCGCGACTGGACCTCGATTTTCTCCGTGAAGGTTTTGCTCGTTCTCGGAGGACTCCGGCGGAGATAGACCACCTGGCGAAGTCGATGGTGTCGTTGGC[G/A]
GAGAAGGTCTTACAATCTATGGACTGGCGTTGGCCTTCTTGGTAGTCTTTGTATCCTGCGATTGTCATCTTAGGGAAAAGTGTAATATAGCCTTAGACTT

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	99.10%	0.60%	0.36%	0.00%	NA
All Indica	2759	99.90%	0.00%	0.11%	0.00%	NA
All Japonica	1512	97.40%	1.70%	0.93%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.50%	0.00%	0.50%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	95.80%	2.70%	1.43%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	97.10%	2.10%	0.83%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	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
vg0423691960	C -> T	LOC_Os04g39760.1	synonymous_variant ; p.Ala586Ala; LOW	synonymous_codon	Average:47.407; most accessible tissue: Zhenshan97 flag leaf, score: 63.67	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0423691960	2.73E-07	1.22E-09	mr1549_2	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
vg0423691960	NA	5.68E-06	mr1550_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
vg0423691960	NA	1.61E-07	mr1757_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