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Detailed information for vg1208631130:

Variant ID: vg1208631130 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 8631130
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AACGAGAGGAACTTGAGCGCCATTCACTTGGAGATGGAGGCACATCACTTGATCTGGAAGGATGGTTGTCCCCCCATTGGATGTCATGAGGCGCACGCCA[C/T]
CGGTCCTCACTGGTACTTGCCCAGGTTGAGACTCCGATGCTGTGACGTGGAGCTTGGGTCCATCCAGGTGCATCCCAGTTGGCTCCCAACCTGCCTCATA

Reverse complement sequence

TATGAGGCAGGTTGGGAGCCAACTGGGATGCACCTGGATGGACCCAAGCTCCACGTCACAGCATCGGAGTCTCAACCTGGGCAAGTACCAGTGAGGACCG[G/A]
TGGCGTGCGCCTCATGACATCCAATGGGGGGACAACCATCCTTCCAGATCAAGTGATGTGCCTCCATCTCCAAGTGAATGGCGCTCAAGTTCCTCTCGTT

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	83.20%	0.10%	3.45%	13.20%	NA
All Indica	2759	86.50%	0.20%	2.61%	10.69%	NA
All Japonica	1512	75.20%	0.10%	4.56%	20.11%	NA
Aus	269	89.60%	0.00%	4.83%	5.58%	NA
Indica I	595	92.60%	0.50%	3.19%	3.70%	NA
Indica II	465	85.60%	0.00%	4.73%	9.68%	NA
Indica III	913	80.00%	0.00%	0.88%	19.17%	NA
Indica Intermediate	786	90.10%	0.30%	2.93%	6.74%	NA
Temperate Japonica	767	86.30%	0.00%	4.82%	8.87%	NA
Tropical Japonica	504	68.10%	0.40%	4.56%	26.98%	NA
Japonica Intermediate	241	54.80%	0.00%	3.73%	41.49%	NA
VI/Aromatic	96	86.50%	0.00%	5.21%	8.33%	NA
Intermediate	90	93.30%	0.00%	4.44%	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
vg1208631130	C -> DEL	N	N	silent_mutation	Average:10.553; most accessible tissue: Callus, score: 25.256	N	N	N	N
vg1208631130	C -> T	LOC_Os12g15120.1	upstream_gene_variant ; 1308.0bp to feature; MODIFIER	silent_mutation	Average:10.553; most accessible tissue: Callus, score: 25.256	N	N	N	N
vg1208631130	C -> T	LOC_Os12g15140.1	downstream_gene_variant ; 1801.0bp to feature; MODIFIER	silent_mutation	Average:10.553; most accessible tissue: Callus, score: 25.256	N	N	N	N
vg1208631130	C -> T	LOC_Os12g15130.1	intron_variant ; MODIFIER	silent_mutation	Average:10.553; most accessible tissue: Callus, score: 25.256	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1208631130	NA	3.25E-07	mr1277	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
vg1208631130	6.88E-06	NA	mr1156_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
vg1208631130	NA	1.43E-08	mr1156_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
vg1208631130	NA	6.04E-06	mr1851_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
vg1208631130	NA	1.30E-06	mr1860_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
vg1208631130	NA	2.42E-08	mr1952_2	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
vg1208631130	NA	1.21E-06	mr1980_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