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Detailed information for vg0622747039:

Variant ID: vg0622747039 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 22747039
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAAATTTCTACAAAATTTTCTAGGTATATGCACCTTGGTGCACAAGGATTCCAGAAGATAAATGCTCAAGTTGTAGACCTAAGCAAAATTTGGTTTGACC[C/T]
AAATCCTTCATCTCAAATTCCGTCTTTAAATGATGACGTGCTTCATTAATATCTTGTGTATTGCCAATAATGTTGAGATCATCGACATATACCGAGATAA

Reverse complement sequence

TTATCTCGGTATATGTCGATGATCTCAACATTATTGGCAATACACAAGATATTAATGAAGCACGTCATCATTTAAAGACGGAATTTGAGATGAAGGATTT[G/A]
GGTCAAACCAAATTTTGCTTAGGTCTACAACTTGAGCATTTATCTTCTGGAATCCTTGTGCACCAAGGTGCATATACCTAGAAAATTTTGTAGAAATTTA

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	18.00%	1.30%	11.53%	69.21%	NA
All Indica	2759	10.10%	2.10%	14.32%	73.43%	NA
All Japonica	1512	34.50%	0.00%	2.84%	62.70%	NA
Aus	269	11.50%	1.10%	31.97%	55.39%	NA
Indica I	595	14.60%	2.00%	13.11%	70.25%	NA
Indica II	465	15.30%	1.70%	9.46%	73.55%	NA
Indica III	913	3.70%	2.20%	19.61%	74.48%	NA
Indica Intermediate	786	11.20%	2.30%	11.96%	74.55%	NA
Temperate Japonica	767	58.70%	0.00%	1.04%	40.29%	NA
Tropical Japonica	504	6.70%	0.00%	3.97%	89.29%	NA
Japonica Intermediate	241	15.40%	0.00%	6.22%	78.42%	NA
VI/Aromatic	96	2.10%	0.00%	2.08%	95.83%	NA
Intermediate	90	16.70%	0.00%	21.11%	62.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0622747039	C -> T	LOC_Os06g38400.1	synonymous_variant ; p.Leu812Leu; LOW	synonymous_codon	Average:7.523; most accessible tissue: Callus, score: 33.213	N	N	N	N
vg0622747039	C -> DEL	LOC_Os06g38400.1	N	frameshift_variant	Average:7.523; most accessible tissue: Callus, score: 33.213	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0622747039	NA	2.88E-06	mr1155	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
vg0622747039	NA	4.30E-06	mr1229	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
vg0622747039	8.23E-06	8.23E-06	mr1710	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
vg0622747039	NA	2.93E-06	mr1741	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
vg0622747039	NA	5.63E-06	mr1782	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
vg0622747039	NA	3.41E-07	mr1881	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
vg0622747039	NA	1.76E-06	mr1887	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
vg0622747039	NA	8.59E-08	mr1887	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