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Detailed information for vg0728664025:

Variant ID: vg0728664025 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 28664025
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

TTATACCAGAATTCAGCAAGATACTACCAAGATGCCCACTTCCTTGGAGTAGCATGCACAAAGCAACGAAGATAAATTTCCAGACACTGATTAACTCGTT[C/T]
GGTTTGCCCATCCGTTTGAGGATGATAAGCTGAACTTTTATGCAGTTTAGTTCCAGACTTAGAGAAGAGCTGCTCCCAAAATTGACTCGTGAAAATCTTA

Reverse complement sequence

TAAGATTTTCACGAGTCAATTTTGGGAGCAGCTCTTCTCTAAGTCTGGAACTAAACTGCATAAAAGTTCAGCTTATCATCCTCAAACGGATGGGCAAACC[G/A]
AACGAGTTAATCAGTGTCTGGAAATTTATCTTCGTTGCTTTGTGCATGCTACTCCAAGGAAGTGGGCATCTTGGTAGTATCTTGCTGAATTCTGGTATAA

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	91.00%	3.50%	2.71%	2.79%	NA
All Indica	2759	85.80%	5.90%	4.60%	3.62%	NA
All Japonica	1512	99.50%	0.00%	0.00%	0.53%	NA
Aus	269	94.80%	0.00%	0.00%	5.20%	NA
Indica I	595	59.80%	23.00%	15.97%	1.18%	NA
Indica II	465	95.30%	1.70%	1.29%	1.72%	NA
Indica III	913	93.10%	0.10%	0.55%	6.24%	NA
Indica Intermediate	786	91.50%	2.30%	2.67%	3.56%	NA
Temperate Japonica	767	99.10%	0.00%	0.00%	0.91%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	97.90%	0.00%	1.04%	1.04%	NA
Intermediate	90	90.00%	0.00%	0.00%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0728664025	C -> DEL	N	N	silent_mutation	Average:47.514; most accessible tissue: Callus, score: 78.953	N	N	N	N
vg0728664025	C -> T	LOC_Os07g47990.1	downstream_gene_variant ; 2115.0bp to feature; MODIFIER	silent_mutation	Average:47.514; most accessible tissue: Callus, score: 78.953	N	N	N	N
vg0728664025	C -> T	LOC_Os07g47990.2	downstream_gene_variant ; 2115.0bp to feature; MODIFIER	silent_mutation	Average:47.514; most accessible tissue: Callus, score: 78.953	N	N	N	N
vg0728664025	C -> T	LOC_Os07g48000.1	intron_variant ; MODIFIER	silent_mutation	Average:47.514; most accessible tissue: Callus, score: 78.953	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0728664025	4.11E-06	NA	mr1183_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
vg0728664025	4.90E-06	NA	mr1183_2	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
vg0728664025	NA	7.38E-07	mr1233_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
vg0728664025	NA	7.47E-06	mr1291_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
vg0728664025	5.11E-06	NA	mr1364_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
vg0728664025	NA	7.85E-09	mr1558_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
vg0728664025	NA	3.12E-09	mr1709_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
vg0728664025	NA	1.65E-10	mr1962_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