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Detailed information for vg0619381858:

Variant ID: vg0619381858 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 19381858
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCCCGCATCGCAGGCATCCCATCGATCTTCGCGAAACTATAAACCAGCGCCGCGCGGCGAGAGGCTACATCCCCCACCATTCACCATATCGCTATGACGA[C/T]
GACGTGGATGGAGTTGCTGCCTTCACAAGCGACCTGCATCGAGTGGATTGGCCGGCCGGCTTCAAGCCGACTAGAATCGAGAAGTATGATGGCACCACTA

Reverse complement sequence

TAGTGGTGCCATCATACTTCTCGATTCTAGTCGGCTTGAAGCCGGCCGGCCAATCCACTCGATGCAGGTCGCTTGTGAAGGCAGCAACTCCATCCACGTC[G/A]
TCGTCATAGCGATATGGTGAATGGTGGGGGATGTAGCCTCTCGCCGCGCGGCGCTGGTTTATAGTTTCGCGAAGATCGATGGGATGCCTGCGATGCGGGG

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	86.00%	13.60%	0.21%	0.25%	NA
All Indica	2759	84.70%	14.60%	0.33%	0.36%	NA
All Japonica	1512	96.50%	3.50%	0.00%	0.00%	NA
Aus	269	34.60%	64.30%	0.37%	0.74%	NA
Indica I	595	87.10%	12.30%	0.17%	0.50%	NA
Indica II	465	99.10%	0.90%	0.00%	0.00%	NA
Indica III	913	73.50%	25.30%	0.55%	0.66%	NA
Indica Intermediate	786	87.30%	12.20%	0.38%	0.13%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	89.90%	10.10%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	91.10%	8.90%	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
vg0619381858	C -> T	LOC_Os06g33290.1	synonymous_variant ; p.Asp385Asp; LOW	synonymous_codon	Average:63.961; most accessible tissue: Minghui63 flag leaf, score: 76.807	N	N	N	N
vg0619381858	C -> DEL	LOC_Os06g33290.1	N	frameshift_variant	Average:63.961; most accessible tissue: Minghui63 flag leaf, score: 76.807	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0619381858	NA	9.87E-06	mr1043	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
vg0619381858	4.69E-06	5.67E-08	mr1738	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
vg0619381858	NA	4.67E-07	mr1835	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
vg0619381858	NA	4.22E-06	mr1236_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
vg0619381858	NA	7.00E-09	mr1327_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
vg0619381858	NA	4.26E-09	mr1327_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