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Detailed information for vg1125635728:

Variant ID: vg1125635728 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25635728
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:

TGCTCAAGCTTACAAGCAAGAGGGTGAATAAAGATGCAAACCAGATTTTCCGTGACATCTTGGACAAGTGTTATCCAAGCGAATTCTGCATGAAGATCTT[C/T]
GCTCACGCCCTCTACGCCAATCCCAACAGAAGCAAACAAGATCTACGCAAGTTGCTTGATTCCCTGGATTCAAAAAAATCACTAGGCATCAATGCTAAGA

Reverse complement sequence

TCTTAGCATTGATGCCTAGTGATTTTTTTGAATCCAGGGAATCAAGCAACTTGCGTAGATCTTGTTTGCTTCTGTTGGGATTGGCGTAGAGGGCGTGAGC[G/A]
AAGATCTTCATGCAGAATTCGCTTGGATAACACTTGTCCAAGATGTCACGGAAAATCTGGTTTGCATCTTTATTCACCCTCTTGCTTGTAAGCTTGAGCA

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	79.80%	1.90%	0.72%	17.60%	NA
All Indica	2759	72.50%	0.30%	0.98%	26.31%	NA
All Japonica	1512	96.20%	2.40%	0.26%	1.19%	NA
Aus	269	55.40%	15.60%	1.12%	27.88%	NA
Indica I	595	85.50%	0.00%	0.00%	14.45%	NA
Indica II	465	87.30%	0.00%	0.65%	12.04%	NA
Indica III	913	66.80%	0.20%	0.99%	31.98%	NA
Indica Intermediate	786	60.30%	0.60%	1.91%	37.15%	NA
Temperate Japonica	767	94.80%	3.40%	0.39%	1.43%	NA
Tropical Japonica	504	99.20%	0.40%	0.00%	0.40%	NA
Japonica Intermediate	241	94.20%	3.30%	0.41%	2.07%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	83.30%	2.20%	0.00%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1125635728	C -> T	LOC_Os11g42590.1	synonymous_variant ; p.Phe750Phe; LOW	synonymous_codon	Average:28.253; most accessible tissue: Zhenshan97 root, score: 54.262	N	N	N	N
vg1125635728	C -> DEL	LOC_Os11g42590.1	N	frameshift_variant	Average:28.253; most accessible tissue: Zhenshan97 root, score: 54.262	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125635728	8.01E-07	8.01E-07	mr1644	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
vg1125635728	2.47E-07	2.59E-07	mr1038_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
vg1125635728	6.10E-10	6.10E-10	mr1191_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