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Detailed information for vg0106964159:

Variant ID: vg0106964159 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 6964159
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACGGCCCTATTCTTTTCTCCAACAAAAGTTGGATAAACTTTTAGATAAAAGTGACATGCTTTTCAAACTGCTAAACGGTGCATTTTGTGCGAAAACTTTC[T/G]
ATATAAAAGTTGTTCTAAAGTATCAGATTAATACAAATTTCAAGTTTGTAATAATTAAAACTCAATTAATCACACGTAATTACCACCTCGTTTTGCATGA

Reverse complement sequence

TCATGCAAAACGAGGTGGTAATTACGTGTGATTAATTGAGTTTTAATTATTACAAACTTGAAATTTGTATTAATCTGATACTTTAGAACAACTTTTATAT[A/C]
GAAAGTTTTCGCACAAAATGCACCGTTTAGCAGTTTGAAAAGCATGTCACTTTTATCTAAAAGTTTATCCAACTTTTGTTGGAGAAAAGAATAGGGCCGT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	96.80%	2.70%	0.57%	0.00%	NA
All Indica	2759	94.80%	4.50%	0.69%	0.00%	NA
All Japonica	1512	99.80%	0.10%	0.13%	0.00%	NA
Aus	269	98.50%	0.00%	1.49%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	77.40%	18.90%	3.66%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	95.20%	4.60%	0.25%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.20%	0.40%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	0.00%	2.22%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0106964159	T -> G	LOC_Os01g12650.1	upstream_gene_variant ; 3461.0bp to feature; MODIFIER	silent_mutation	Average:42.147; most accessible tissue: Minghui63 panicle, score: 76.913	N	N	N	N
vg0106964159	T -> G	LOC_Os01g12640-LOC_Os01g12650	intergenic_region ; MODIFIER	silent_mutation	Average:42.147; most accessible tissue: Minghui63 panicle, score: 76.913	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0106964159	2.54E-08	1.08E-10	mr1310	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
vg0106964159	4.35E-14	3.23E-27	mr1498	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
vg0106964159	5.90E-10	3.24E-23	mr1769	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
vg0106964159	5.89E-06	5.89E-06	mr1916	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
vg0106964159	4.85E-08	9.38E-13	mr1925	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
vg0106964159	2.04E-11	2.67E-19	mr1951	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
vg0106964159	2.10E-08	1.86E-13	mr1310_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
vg0106964159	1.51E-10	2.07E-21	mr1498_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
vg0106964159	5.52E-09	5.95E-26	mr1769_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
vg0106964159	NA	6.83E-07	mr1916_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
vg0106964159	4.03E-08	6.78E-12	mr1925_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
vg0106964159	3.89E-08	1.66E-14	mr1951_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