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Detailed information for vg0507253850:

Variant ID: vg0507253850 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 7253850
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTATTGAATAAAGTCTTACAAGAGAGGAAGAGCTACTAGAACCATACCCGACTTCTCTGCAAGACATGAAGAACTAAGGAAGAATATTTAATTCTAACT[C/T]
TACTAGCACTAGAGCAAAATATGTAAACTAGGGTTGCGCTCGTTACCTCCTGTTCCCAACTTCCCTTCCTCGTTTTCCACGCGCACGCTTTTCAAACTGC

Reverse complement sequence

GCAGTTTGAAAAGCGTGCGCGTGGAAAACGAGGAAGGGAAGTTGGGAACAGGAGGTAACGAGCGCAACCCTAGTTTACATATTTTGCTCTAGTGCTAGTA[G/A]
AGTTAGAATTAAATATTCTTCCTTAGTTCTTCATGTCTTGCAGAGAAGTCGGGTATGGTTCTAGTAGCTCTTCCTCTCTTGTAAGACTTTATTCAATAAT

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	54.70%	7.00%	1.69%	36.58%	NA
All Indica	2759	58.10%	5.70%	1.92%	34.29%	NA
All Japonica	1512	57.10%	0.70%	1.19%	41.01%	NA
Aus	269	21.90%	58.70%	1.49%	17.84%	NA
Indica I	595	73.30%	10.30%	0.17%	16.30%	NA
Indica II	465	31.40%	0.20%	3.44%	64.95%	NA
Indica III	913	59.30%	4.20%	2.74%	33.84%	NA
Indica Intermediate	786	61.20%	7.10%	1.40%	30.28%	NA
Temperate Japonica	767	91.40%	0.40%	0.52%	7.69%	NA
Tropical Japonica	504	13.50%	0.60%	1.98%	83.93%	NA
Japonica Intermediate	241	39.40%	1.70%	1.66%	57.26%	NA
VI/Aromatic	96	15.60%	2.10%	2.08%	80.21%	NA
Intermediate	90	47.80%	6.70%	3.33%	42.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0507253850	C -> T	LOC_Os05g12640.1	upstream_gene_variant ; 1659.0bp to feature; MODIFIER	silent_mutation	Average:33.899; most accessible tissue: Zhenshan97 root, score: 44.635	N	N	N	N
vg0507253850	C -> T	LOC_Os05g12640.2	upstream_gene_variant ; 1659.0bp to feature; MODIFIER	silent_mutation	Average:33.899; most accessible tissue: Zhenshan97 root, score: 44.635	N	N	N	N
vg0507253850	C -> T	LOC_Os05g12640.4	upstream_gene_variant ; 1659.0bp to feature; MODIFIER	silent_mutation	Average:33.899; most accessible tissue: Zhenshan97 root, score: 44.635	N	N	N	N
vg0507253850	C -> T	LOC_Os05g12640.6	upstream_gene_variant ; 1659.0bp to feature; MODIFIER	silent_mutation	Average:33.899; most accessible tissue: Zhenshan97 root, score: 44.635	N	N	N	N
vg0507253850	C -> T	LOC_Os05g12640.3	upstream_gene_variant ; 1661.0bp to feature; MODIFIER	silent_mutation	Average:33.899; most accessible tissue: Zhenshan97 root, score: 44.635	N	N	N	N
vg0507253850	C -> T	LOC_Os05g12630.1	downstream_gene_variant ; 2453.0bp to feature; MODIFIER	silent_mutation	Average:33.899; most accessible tissue: Zhenshan97 root, score: 44.635	N	N	N	N
vg0507253850	C -> T	LOC_Os05g12630.2	downstream_gene_variant ; 2453.0bp to feature; MODIFIER	silent_mutation	Average:33.899; most accessible tissue: Zhenshan97 root, score: 44.635	N	N	N	N
vg0507253850	C -> T	LOC_Os05g12630-LOC_Os05g12640	intergenic_region ; MODIFIER	silent_mutation	Average:33.899; most accessible tissue: Zhenshan97 root, score: 44.635	N	N	N	N
vg0507253850	C -> DEL	N	N	silent_mutation	Average:33.899; most accessible tissue: Zhenshan97 root, score: 44.635	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0507253850	NA	2.88E-08	mr1039	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
vg0507253850	NA	1.72E-06	mr1126	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
vg0507253850	NA	1.11E-06	mr1397	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
vg0507253850	9.30E-06	NA	mr1039_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
vg0507253850	1.78E-06	5.28E-08	mr1039_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
vg0507253850	6.59E-08	1.23E-06	mr1632_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