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Detailed information for vg0626990911:

Variant ID: vg0626990911 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 26990911
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

CATATAAGACAGGTGAACAAGGGCAGGCGATGATGGAAAGAAACAAAGAAAATGCCATCAAGAAGAAGTACCATCACCACTTGGTGTCAGGCGGCTATAG[C/T]
GTCGCGATGCCGAAGTGGGAGGAGATGGAGGCTAGCTTGCTTGAGAGGGGTATCGAACCGGCCACCGCTAATTGGCCGGAACGATCGAAGTTCTGGTACT

Reverse complement sequence

AGTACCAGAACTTCGATCGTTCCGGCCAATTAGCGGTGGCCGGTTCGATACCCCTCTCAAGCAAGCTAGCCTCCATCTCCTCCCACTTCGGCATCGCGAC[G/A]
CTATAGCCGCCTGACACCAAGTGGTGATGGTACTTCTTCTTGATGGCATTTTCTTTGTTTCTTTCCATCATCGCCTGCCCTTGTTCACCTGTCTTATATG

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	43.60%	6.10%	2.07%	48.31%	NA
All Indica	2759	18.80%	4.50%	3.12%	73.54%	NA
All Japonica	1512	95.60%	0.40%	0.07%	3.90%	NA
Aus	269	15.60%	50.60%	2.97%	30.86%	NA
Indica I	595	7.90%	0.20%	2.52%	89.41%	NA
Indica II	465	15.10%	2.40%	3.44%	79.14%	NA
Indica III	913	24.10%	7.60%	3.50%	64.84%	NA
Indica Intermediate	786	23.20%	5.60%	2.93%	68.32%	NA
Temperate Japonica	767	99.10%	0.00%	0.13%	0.78%	NA
Tropical Japonica	504	90.10%	1.00%	0.00%	8.93%	NA
Japonica Intermediate	241	96.30%	0.40%	0.00%	3.32%	NA
VI/Aromatic	96	6.20%	10.40%	2.08%	81.25%	NA
Intermediate	90	51.10%	10.00%	1.11%	37.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0626990911	C -> T	LOC_Os06g44710.1	synonymous_variant ; p.Ser276Ser; LOW	synonymous_codon	Average:5.613; most accessible tissue: Callus, score: 14.105	N	N	N	N
vg0626990911	C -> DEL	LOC_Os06g44710.1	N	frameshift_variant	Average:5.613; most accessible tissue: Callus, score: 14.105	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0626990911	4.79E-06	NA	mr1006_2	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