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Detailed information for vg0107540499:

Variant ID: vg0107540499 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 7540499
Reference Allele: C	Alternative Allele: G
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTTAAAAACATGCAATCTCAATTACTTTTAGCTCAAAATTATATCAAATTGTTTTAATTTTGTACGTATTATGTAACTTAATTTTCTACAGCAACGCGAC[C/G]
AGATGTTCATATAGTATCTTATAAAAGTATGAGCAGTACTAGAATACTAAAACTGGAGAATACCGAATGTACTTACTTATAAACTGTAGGGGAAATTAAA

Reverse complement sequence

TTTAATTTCCCCTACAGTTTATAAGTAAGTACATTCGGTATTCTCCAGTTTTAGTATTCTAGTACTGCTCATACTTTTATAAGATACTATATGAACATCT[G/C]
GTCGCGTTGCTGTAGAAAATTAAGTTACATAATACGTACAAAATTAAAACAATTTGATATAATTTTGAGCTAAAAGTAATTGAGATTGCATGTTTTTAAG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	73.30%	26.40%	0.30%	0.00%	NA
All Indica	2759	99.40%	0.40%	0.18%	0.00%	NA
All Japonica	1512	23.90%	75.50%	0.53%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	99.30%	0.20%	0.50%	0.00%	NA
Indica II	465	99.60%	0.20%	0.22%	0.00%	NA
Indica III	913	99.60%	0.40%	0.00%	0.00%	NA
Indica Intermediate	786	99.20%	0.60%	0.13%	0.00%	NA
Temperate Japonica	767	4.00%	95.70%	0.26%	0.00%	NA
Tropical Japonica	504	57.90%	40.90%	1.19%	0.00%	NA
Japonica Intermediate	241	16.20%	83.80%	0.00%	0.00%	NA
VI/Aromatic	96	24.00%	75.00%	1.04%	0.00%	NA
Intermediate	90	74.40%	25.60%	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
vg0107540499	C -> G	LOC_Os01g13510.1	upstream_gene_variant ; 3172.0bp to feature; MODIFIER	silent_mutation	Average:32.542; most accessible tissue: Callus, score: 50.644	N	N	N	N
vg0107540499	C -> G	LOC_Os01g13500-LOC_Os01g13510	intergenic_region ; MODIFIER	silent_mutation	Average:32.542; most accessible tissue: Callus, score: 50.644	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0107540499	NA	2.83E-06	mr1213	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
vg0107540499	NA	6.70E-07	mr1403	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
vg0107540499	NA	2.18E-10	mr1691	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
vg0107540499	NA	4.50E-11	mr1693	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
vg0107540499	NA	7.30E-07	mr1693	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
vg0107540499	NA	2.43E-13	mr1741	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
vg0107540499	NA	9.20E-06	mr1741	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
vg0107540499	NA	8.16E-18	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
vg0107540499	NA	6.86E-06	mr1224_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
vg0107540499	NA	2.32E-06	mr1246_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
vg0107540499	NA	4.12E-09	mr1624_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
vg0107540499	NA	3.19E-24	mr1679_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
vg0107540499	NA	3.06E-07	mr1679_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
vg0107540499	NA	2.44E-07	mr1691_2	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