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Detailed information for vg0112183141:

Variant ID: vg0112183141 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 12183141
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, G: 0.00, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:

GCATGACATACGTTACGCTCGCCGGCCGATGTCATTGATCAACAAGGTACGTCGTCATTGATCACTGTGTGTTTTTGGCCTAAAAAATGAGTTAGCTATC[C/G]
AAGTCTTTCCCTTTTTTTTAATCCTTACATATACATTGACGTAGCCATTAGAAGTTTGTTTATAATTTCTTTTTCACTGCAACATAACCGGAAAATAGGC

Reverse complement sequence

GCCTATTTTCCGGTTATGTTGCAGTGAAAAAGAAATTATAAACAAACTTCTAATGGCTACGTCAATGTATATGTAAGGATTAAAAAAAAGGGAAAGACTT[G/C]
GATAGCTAACTCATTTTTTAGGCCAAAAACACACAGTGATCAATGACGACGTACCTTGTTGATCAATGACATCGGCCGGCGAGCGTAACGTATGTCATGC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	79.10%	15.40%	0.30%	5.18%	NA
All Indica	2759	72.40%	26.00%	0.25%	1.38%	NA
All Japonica	1512	85.80%	0.10%	0.46%	13.56%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	91.90%	7.90%	0.17%	0.00%	NA
Indica II	465	78.50%	18.50%	0.00%	3.01%	NA
Indica III	913	60.80%	38.30%	0.22%	0.66%	NA
Indica Intermediate	786	67.40%	29.80%	0.51%	2.29%	NA
Temperate Japonica	767	88.00%	0.10%	0.52%	11.34%	NA
Tropical Japonica	504	78.00%	0.20%	0.60%	21.23%	NA
Japonica Intermediate	241	95.40%	0.00%	0.00%	4.56%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	6.70%	0.00%	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
vg0112183141	C -> G	LOC_Os01g21710.1	upstream_gene_variant ; 1716.0bp to feature; MODIFIER	silent_mutation	Average:53.839; most accessible tissue: Zhenshan97 root, score: 80.909	N	N	N	N
vg0112183141	C -> G	LOC_Os01g21720.1	downstream_gene_variant ; 4809.0bp to feature; MODIFIER	silent_mutation	Average:53.839; most accessible tissue: Zhenshan97 root, score: 80.909	N	N	N	N
vg0112183141	C -> G	LOC_Os01g21700-LOC_Os01g21710	intergenic_region ; MODIFIER	silent_mutation	Average:53.839; most accessible tissue: Zhenshan97 root, score: 80.909	N	N	N	N
vg0112183141	C -> DEL	N	N	silent_mutation	Average:53.839; most accessible tissue: Zhenshan97 root, score: 80.909	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0112183141	NA	7.46E-06	mr1071	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
vg0112183141	NA	3.83E-06	mr1080	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
vg0112183141	NA	2.29E-06	mr1200	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
vg0112183141	NA	6.49E-06	mr1395	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
vg0112183141	2.88E-06	2.93E-08	mr1613	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
vg0112183141	NA	4.80E-06	mr1618	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
vg0112183141	NA	9.18E-07	mr1619	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
vg0112183141	NA	6.49E-06	mr1911_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