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Detailed information for vg0105146788:

Variant ID: vg0105146788 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 5146788
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGGGCAATATTTTCTTAAAATATTTACTATAACTAGAAAAAATGCCTGTGCGTTGCAACGTTGCAATGGGTGAGGTTATTTTAATCTTATCATTGTTATA[C/T]
GGTTTAATTAAGGTGAAGTTTACTATGTGAATTTGCTTGAATATATATATATATTTTTAGAAAATCATAAGCTGCAATTAGAAGTCCGATCATCTCAAGT

Reverse complement sequence

ACTTGAGATGATCGGACTTCTAATTGCAGCTTATGATTTTCTAAAAATATATATATATATTCAAGCAAATTCACATAGTAAACTTCACCTTAATTAAACC[G/A]
TATAACAATGATAAGATTAAAATAACCTCACCCATTGCAACGTTGCAACGCACAGGCATTTTTTCTAGTTATAGTAAATATTTTAAGAAAATATTGCCCA

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	92.70%	6.20%	0.42%	0.72%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	78.60%	18.40%	0.86%	2.18%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	85.50%	12.10%	0.39%	1.96%	NA
Tropical Japonica	504	66.30%	30.40%	0.99%	2.38%	NA
Japonica Intermediate	241	82.20%	13.30%	2.07%	2.49%	NA
VI/Aromatic	96	83.30%	9.40%	7.29%	0.00%	NA
Intermediate	90	96.70%	2.20%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0105146788	C -> T	LOC_Os01g09900.1	upstream_gene_variant ; 1906.0bp to feature; MODIFIER	silent_mutation	Average:20.822; most accessible tissue: Callus, score: 31.884	N	N	N	N
vg0105146788	C -> T	LOC_Os01g09890-LOC_Os01g09900	intergenic_region ; MODIFIER	silent_mutation	Average:20.822; most accessible tissue: Callus, score: 31.884	N	N	N	N
vg0105146788	C -> DEL	N	N	silent_mutation	Average:20.822; most accessible tissue: Callus, score: 31.884	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0105146788	4.51E-24	2.32E-26	mr1057	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
vg0105146788	7.06E-14	4.34E-20	mr1057	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
vg0105146788	9.51E-06	NA	mr1238	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
vg0105146788	3.75E-06	NA	mr1677	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
vg0105146788	3.59E-06	4.03E-07	mr1677	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
vg0105146788	2.16E-33	1.17E-38	mr1057_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
vg0105146788	1.58E-18	2.47E-23	mr1057_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
vg0105146788	1.65E-06	NA	mr1238_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
vg0105146788	9.25E-06	NA	mr1484_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
vg0105146788	1.92E-06	NA	mr1841_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