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Detailed information for vg0506413525:

Variant ID: vg0506413525 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 6413525
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATCTCAATGACATGTAGAACCCACATGAGTCAATGACATGTGGGTCAGGGTGGCATATCACATTTTCTGTAAAATTTATGTGGCATGGTTCAAATTTTCC[C/T]
TTAATAAAAATGGTTGCTGAGATTTGCTTAGACAAAGTAGAGGAGGAATTCCCTTTTAATTATCTGTCCCTACCCAGGTATTAAAAAAGAGGGAGTTCCT

Reverse complement sequence

AGGAACTCCCTCTTTTTTAATACCTGGGTAGGGACAGATAATTAAAAGGGAATTCCTCCTCTACTTTGTCTAAGCAAATCTCAGCAACCATTTTTATTAA[G/A]
GGAAAATTTGAACCATGCCACATAAATTTTACAGAAAATGTGATATGCCACCCTGACCCACATGTCATTGACTCATGTGGGTTCTACATGTCATTGAGAT

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	89.40%	4.60%	0.51%	5.56%	NA
All Indica	2759	96.20%	0.10%	0.14%	3.55%	NA
All Japonica	1512	84.90%	13.90%	1.12%	0.07%	NA
Aus	269	38.70%	0.00%	1.12%	60.22%	NA
Indica I	595	96.00%	0.00%	0.17%	3.87%	NA
Indica II	465	98.90%	0.00%	0.00%	1.08%	NA
Indica III	913	99.30%	0.00%	0.00%	0.66%	NA
Indica Intermediate	786	91.20%	0.30%	0.38%	8.14%	NA
Temperate Japonica	767	99.10%	0.80%	0.13%	0.00%	NA
Tropical Japonica	504	60.90%	36.30%	2.78%	0.00%	NA
Japonica Intermediate	241	90.00%	8.70%	0.83%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	4.40%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0506413525	C -> T	LOC_Os05g11340.1	upstream_gene_variant ; 3666.0bp to feature; MODIFIER	silent_mutation	Average:69.196; most accessible tissue: Minghui63 root, score: 87.595	N	N	N	N
vg0506413525	C -> T	LOC_Os05g11350.1	upstream_gene_variant ; 1219.0bp to feature; MODIFIER	silent_mutation	Average:69.196; most accessible tissue: Minghui63 root, score: 87.595	N	N	N	N
vg0506413525	C -> T	LOC_Os05g11360.1	downstream_gene_variant ; 3002.0bp to feature; MODIFIER	silent_mutation	Average:69.196; most accessible tissue: Minghui63 root, score: 87.595	N	N	N	N
vg0506413525	C -> T	LOC_Os05g11340-LOC_Os05g11350	intergenic_region ; MODIFIER	silent_mutation	Average:69.196; most accessible tissue: Minghui63 root, score: 87.595	N	N	N	N
vg0506413525	C -> DEL	N	N	silent_mutation	Average:69.196; most accessible tissue: Minghui63 root, score: 87.595	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0506413525	NA	2.94E-06	mr1304	Jap_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
vg0506413525	NA	3.78E-07	mr1422	Jap_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
vg0506413525	7.81E-06	7.81E-06	mr1501	Jap_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
vg0506413525	1.68E-06	5.35E-11	mr1583	Jap_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
vg0506413525	9.50E-07	NA	mr1754	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
vg0506413525	NA	3.11E-06	mr1124_2	Jap_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
vg0506413525	NA	2.73E-06	mr1422_2	Jap_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
vg0506413525	NA	3.01E-06	mr1583_2	Jap_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
vg0506413525	6.25E-11	4.02E-13	mr1850_2	Jap_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