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Detailed information for vg0109413154:

Variant ID: vg0109413154 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 9413154
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AACAATATTTAAAAATCCTGAGTCATACAGAATATGGCATGATAGGTTAGGACATCCAGGTCTAGGGATGATGACAAGAATCATCTCAACTTCAAATGGC[C/T]
ATAATTTACGAACTAACGATTTCCCAAACCAAGAAGATTTTGTTTGCACTGATTGTGCAACAGCGAAATTAATCGTTAGACCCTCTAATCTAAAGGTGAA

Reverse complement sequence

TTCACCTTTAGATTAGAGGGTCTAACGATTAATTTCGCTGTTGCACAATCAGTGCAAACAAAATCTTCTTGGTTTGGGAAATCGTTAGTTCGTAAATTAT[G/A]
GCCATTTGAAGTTGAGATGATTCTTGTCATCATCCCTAGACCTGGATGTCCTAACCTATCATGCCATATTCTGTATGACTCAGGATTTTTAAATATTGTT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	56.80%	43.10%	0.06%	0.00%	NA
All Indica	2759	89.70%	10.20%	0.11%	0.00%	NA
All Japonica	1512	3.20%	96.80%	0.00%	0.00%	NA
Aus	269	16.40%	83.60%	0.00%	0.00%	NA
Indica I	595	95.30%	4.40%	0.34%	0.00%	NA
Indica II	465	84.70%	15.30%	0.00%	0.00%	NA
Indica III	913	90.00%	10.00%	0.00%	0.00%	NA
Indica Intermediate	786	88.00%	11.80%	0.13%	0.00%	NA
Temperate Japonica	767	1.80%	98.20%	0.00%	0.00%	NA
Tropical Japonica	504	5.40%	94.60%	0.00%	0.00%	NA
Japonica Intermediate	241	3.30%	96.70%	0.00%	0.00%	NA
VI/Aromatic	96	71.90%	28.10%	0.00%	0.00%	NA
Intermediate	90	54.40%	45.60%	0.00%	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
vg0109413154	C -> T	LOC_Os01g16580.1	upstream_gene_variant ; 241.0bp to feature; MODIFIER	silent_mutation	Average:17.69; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N
vg0109413154	C -> T	LOC_Os01g16570.1	downstream_gene_variant ; 801.0bp to feature; MODIFIER	silent_mutation	Average:17.69; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N
vg0109413154	C -> T	LOC_Os01g16570-LOC_Os01g16580	intergenic_region ; MODIFIER	silent_mutation	Average:17.69; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0109413154	2.01E-06	NA	mr1246	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
vg0109413154	NA	3.02E-16	mr1916	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