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Detailed information for vg1217448800:

Variant ID: vg1217448800 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 17448800
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAATTGACTCGTTGAGTCGGTATCTCGTGAGGTTCGCTTGCAAGATTAATCTTAGCCATCCAAAATCAATATAAATCATTTCCTCTCTTTTCAGTGGCAT[A/C]
TTATTTCTTTTTAATATATGTCATCTACCAAATATAGTCTAATCTATTTCCGGAGGTTGCTTTAATCTTTTATCTCAGTTATAAATCTTTTGTAAATTGT

Reverse complement sequence

ACAATTTACAAAAGATTTATAACTGAGATAAAAGATTAAAGCAACCTCCGGAAATAGATTAGACTATATTTGGTAGATGACATATATTAAAAAGAAATAA[T/G]
ATGCCACTGAAAAGAGAGGAAATGATTTATATTGATTTTGGATGGCTAAGATTAATCTTGCAAGCGAACCTCACGAGATACCGACTCAACGAGTCAATTC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	90.40%	1.90%	0.89%	6.79%	NA
All Indica	2759	94.10%	0.10%	0.11%	5.65%	NA
All Japonica	1512	83.30%	5.70%	2.51%	8.53%	NA
Aus	269	99.60%	0.00%	0.00%	0.37%	NA
Indica I	595	96.00%	0.00%	0.17%	3.87%	NA
Indica II	465	98.90%	0.00%	0.00%	1.08%	NA
Indica III	913	90.30%	0.00%	0.11%	9.64%	NA
Indica Intermediate	786	94.30%	0.50%	0.13%	5.09%	NA
Temperate Japonica	767	78.00%	10.30%	2.61%	9.13%	NA
Tropical Japonica	504	89.90%	0.00%	1.59%	8.53%	NA
Japonica Intermediate	241	86.30%	2.90%	4.15%	6.64%	NA
VI/Aromatic	96	68.80%	0.00%	1.04%	30.21%	NA
Intermediate	90	91.10%	2.20%	0.00%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1217448800	A -> C	LOC_Os12g29380.1	downstream_gene_variant ; 4559.0bp to feature; MODIFIER	silent_mutation	Average:45.079; most accessible tissue: Zhenshan97 panicle, score: 67.02	N	N	N	N
vg1217448800	A -> C	LOC_Os12g29370-LOC_Os12g29380	intergenic_region ; MODIFIER	silent_mutation	Average:45.079; most accessible tissue: Zhenshan97 panicle, score: 67.02	N	N	N	N
vg1217448800	A -> DEL	N	N	silent_mutation	Average:45.079; most accessible tissue: Zhenshan97 panicle, score: 67.02	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1217448800	NA	2.26E-06	mr1616	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
vg1217448800	NA	4.52E-06	mr1697	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
vg1217448800	NA	6.29E-07	mr1851	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
vg1217448800	3.26E-06	3.26E-06	mr1004_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
vg1217448800	NA	8.43E-06	mr1296_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
vg1217448800	4.02E-06	4.02E-06	mr1469_2	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