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Detailed information for vg0528474996:

Variant ID: vg0528474996 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 28474996
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCGAGACGGCGGCGGAGGGAGTTGGAGGCAGTAAGGCGGCGGCGAGGCGGCGAACGTCTTCCGAGGAGAGCTGGCCGCCGTTCTGCAGGAGCAGCGGCGT[C/T]
GTCATGGCTCTGCTAGAGCTGAGGAACTCCACTTGTTCGTCCGGTTTGGGGTGCCGGGCCGCCGCGGCGGCGGCGGCGTAGGACTCCTGGATAGTGCAGG

Reverse complement sequence

CCTGCACTATCCAGGAGTCCTACGCCGCCGCCGCCGCGGCGGCCCGGCACCCCAAACCGGACGAACAAGTGGAGTTCCTCAGCTCTAGCAGAGCCATGAC[G/A]
ACGCCGCTGCTCCTGCAGAACGGCGGCCAGCTCTCCTCGGAAGACGTTCGCCGCCTCGCCGCCGCCTTACTGCCTCCAACTCCCTCCGCCGCCGTCTCGC

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	97.00%	2.10%	0.95%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	90.60%	6.40%	2.98%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	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	86.00%	8.30%	5.61%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	86.70%	12.40%	0.83%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0528474996	C -> T	LOC_Os05g49630.1	synonymous_variant ; p.Thr400Thr; LOW	synonymous_codon	Average:74.077; most accessible tissue: Zhenshan97 young leaf, score: 81.353	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0528474996	1.33E-06	1.86E-07	mr1092_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