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Detailed information for vg0616628658:

Variant ID: vg0616628658 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 16628658
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGAGAAGCTTGCCCACAGGTACACCAAACACACACTTATCGGGGTTCAGTTTTATGCGGGCGGAGCGGAGATTCTCAAAAGTTTCCGCTAGATCTGAGAG[T/C]
AAAGTCTCTTGATTGCGCGTTTTTACAACCAAGTCATCGACATAAGCCTCAACATTACGTCCTAATTGGCTACCCAAAGAAATTCGAGTAGCGCGTTGAA

Reverse complement sequence

TTCAACGCGCTACTCGAATTTCTTTGGGTAGCCAATTAGGACGTAATGTTGAGGCTTATGTCGATGACTTGGTTGTAAAAACGCGCAATCAAGAGACTTT[A/G]
CTCTCAGATCTAGCGGAAACTTTTGAGAATCTCCGCTCCGCCCGCATAAAACTGAACCCCGATAAGTGTGTGTTTGGTGTACCTGTGGGCAAGCTTCTCG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	34.00%	0.70%	6.96%	58.32%	NA
All Indica	2759	3.60%	1.20%	6.20%	89.02%	NA
All Japonica	1512	95.80%	0.10%	2.58%	1.52%	NA
Aus	269	2.60%	0.00%	17.10%	80.30%	NA
Indica I	595	4.40%	0.30%	7.06%	88.24%	NA
Indica II	465	2.20%	0.60%	4.52%	92.69%	NA
Indica III	913	2.20%	2.40%	5.70%	89.70%	NA
Indica Intermediate	786	5.30%	0.90%	7.12%	86.64%	NA
Temperate Japonica	767	96.50%	0.00%	1.04%	2.48%	NA
Tropical Japonica	504	95.00%	0.00%	4.56%	0.40%	NA
Japonica Intermediate	241	95.40%	0.40%	3.32%	0.83%	NA
VI/Aromatic	96	16.70%	0.00%	56.25%	27.08%	NA
Intermediate	90	40.00%	0.00%	21.11%	38.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0616628658	T -> C	LOC_Os06g29140.1	synonymous_variant ; p.Leu967Leu; LOW	synonymous_codon	Average:9.355; most accessible tissue: Callus, score: 27.307	N	N	N	N
vg0616628658	T -> DEL	LOC_Os06g29140.1	N	frameshift_variant	Average:9.355; most accessible tissue: Callus, score: 27.307	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0616628658	1.62E-06	4.20E-07	mr1912	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
vg0616628658	NA	5.96E-06	mr1043_2	Ind_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