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Detailed information for vg0517733960:

Variant ID: vg0517733960 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 17733960
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, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:

GCTCTTTTCTAGCCTTTCTAAAGCAGAAACCTACCAAATGACCAGCTTTCCCACAATAGGTGCACTCATACTTGGTTTTCTCTACAGGCTTGGTTTGTTT[C/T]
TGGTTTTGCTTGTGCTCAACTTGTTTTGGATTTTTGGGTCTAGGTAACTCTATAGGCTTAGACTTGCTAGTCATAGGTACCATCTTTGGTTCTGAGGTTT

Reverse complement sequence

AAACCTCAGAACCAAAGATGGTACCTATGACTAGCAAGTCTAAGCCTATAGAGTTACCTAGACCCAAAAATCCAAAACAAGTTGAGCACAAGCAAAACCA[G/A]
AAACAAACCAAGCCTGTAGAGAAAACCAAGTATGAGTGCACCTATTGTGGGAAAGCTGGTCATTTGGTAGGTTTCTGCTTTAGAAAGGCTAGAAAAGAGC

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	95.50%	3.60%	0.44%	0.42%	NA
All Indica	2759	99.60%	0.30%	0.11%	0.00%	NA
All Japonica	1512	92.90%	4.80%	0.99%	1.26%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	99.10%	0.60%	0.25%	0.00%	NA
Temperate Japonica	767	96.60%	2.10%	0.65%	0.65%	NA
Tropical Japonica	504	90.90%	4.40%	1.98%	2.78%	NA
Japonica Intermediate	241	85.50%	14.50%	0.00%	0.00%	NA
VI/Aromatic	96	10.40%	88.50%	1.04%	0.00%	NA
Intermediate	90	90.00%	6.70%	2.22%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0517733960	C -> T	LOC_Os05g30610.1	synonymous_variant ; p.Gln614Gln; LOW	synonymous_codon	Average:13.515; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0517733960	C -> DEL	LOC_Os05g30610.1	N	frameshift_variant	Average:13.515; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0517733960	NA	9.44E-06	mr1438	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
vg0517733960	8.35E-06	NA	mr1740	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
vg0517733960	1.20E-06	1.20E-06	mr1994	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
vg0517733960	NA	2.66E-07	mr1057_2	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