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Detailed information for vg0619153237:

Variant ID: vg0619153237 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 19153237
Reference Allele: A	Alternative Allele: T
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

GCAATGTTTTTCGTGATTAGTCTCACATTACACATTGATGATAATTGTGATAAATAATTTGACTCCTGGTTTGGAATGGTATATTCCTGGTATGGAGGTT[A/T]
GATTTGTACAACCGGGGTTGGTTGTTCAAATAAGGTTGGGCCTATGTAACACGGGTGTGTTGTATGGTGTTTATCTAATACTGTTTAATTATTCAACTGT

Reverse complement sequence

ACAGTTGAATAATTAAACAGTATTAGATAAACACCATACAACACACCCGTGTTACATAGGCCCAACCTTATTTGAACAACCAACCCCGGTTGTACAAATC[T/A]
AACCTCCATACCAGGAATATACCATTCCAAACCAGGAGTCAAATTATTTATCACAATTATCATCAATGTGTAATGTGAGACTAATCACGAAAAACATTGC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	66.30%	31.10%	2.41%	0.21%	NA
All Indica	2759	94.30%	2.80%	2.90%	0.00%	NA
All Japonica	1512	7.60%	89.70%	1.98%	0.66%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	93.80%	1.70%	4.54%	0.00%	NA
Indica II	465	95.10%	3.90%	1.08%	0.00%	NA
Indica III	913	97.80%	0.90%	1.31%	0.00%	NA
Indica Intermediate	786	90.10%	5.30%	4.58%	0.00%	NA
Temperate Japonica	767	5.00%	92.30%	1.43%	1.30%	NA
Tropical Japonica	504	12.10%	86.70%	1.19%	0.00%	NA
Japonica Intermediate	241	6.60%	88.00%	5.39%	0.00%	NA
VI/Aromatic	96	94.80%	4.20%	1.04%	0.00%	NA
Intermediate	90	64.40%	32.20%	3.33%	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
vg0619153237	A -> T	LOC_Os06g32900.1	splice_region_variant&intron_variant ; LOW	silent_mutation	Average:49.351; most accessible tissue: Minghui63 flag leaf, score: 75.341	N	N	N	N
vg0619153237	A -> T	LOC_Os06g32910.1	downstream_gene_variant ; 4001.0bp to feature; MODIFIER	silent_mutation	Average:49.351; most accessible tissue: Minghui63 flag leaf, score: 75.341	N	N	N	N
vg0619153237	A -> DEL	N	N	silent_mutation	Average:49.351; most accessible tissue: Minghui63 flag leaf, score: 75.341	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0619153237	2.37E-06	NA	mr1071	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
vg0619153237	4.23E-06	NA	mr1140	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
vg0619153237	NA	9.20E-10	mr1354	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
vg0619153237	9.63E-06	NA	mr1395	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
vg0619153237	NA	4.22E-06	mr1408	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
vg0619153237	8.15E-06	NA	mr1618	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
vg0619153237	NA	4.40E-21	mr1676	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
vg0619153237	NA	3.71E-16	mr1900	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
vg0619153237	NA	1.18E-06	mr1900	Jap_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
vg0619153237	NA	3.07E-21	mr1042_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
vg0619153237	NA	3.50E-10	mr1354_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
vg0619153237	NA	2.05E-06	mr1479_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
vg0619153237	NA	2.26E-11	mr1667_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
vg0619153237	NA	5.38E-08	mr1681_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