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Detailed information for vg1217281529:

Variant ID: vg1217281529 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 17281529
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TATTTTTGTGTGCGGTGGTTCCGCCCGTCTGGAATCCATCGTCTGCCAAAATCACGATTTTTTCGTACGGGTGAGGCACCGCCCACGAAAATCGATTTTC[G/A]
CGGTCGGGCGCTTAAGCCGCCCCCACGGTAAAATAAAAAATCAAAACAAAAAAAAGAAAAAACCAAAACCCTAACTGCCGCCGTCGTCGTCGCCCTCTTC

Reverse complement sequence

GAAGAGGGCGACGACGACGGCGGCAGTTAGGGTTTTGGTTTTTTCTTTTTTTTGTTTTGATTTTTTATTTTACCGTGGGGGCGGCTTAAGCGCCCGACCG[C/T]
GAAAATCGATTTTCGTGGGCGGTGCCTCACCCGTACGAAAAAATCGTGATTTTGGCAGACGATGGATTCCAGACGGGCGGAACCACCGCACACAAAAATA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	91.00%	6.60%	0.17%	2.20%	NA
All Indica	2759	92.10%	4.10%	0.25%	3.55%	NA
All Japonica	1512	87.40%	12.50%	0.07%	0.00%	NA
Aus	269	98.10%	0.00%	0.00%	1.86%	NA
Indica I	595	97.30%	0.20%	0.17%	2.35%	NA
Indica II	465	80.20%	17.60%	0.22%	1.94%	NA
Indica III	913	95.60%	0.40%	0.11%	3.83%	NA
Indica Intermediate	786	91.00%	3.40%	0.51%	5.09%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	69.00%	30.80%	0.20%	0.00%	NA
Japonica Intermediate	241	87.10%	12.90%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	87.80%	11.10%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1217281529	G -> DEL	N	N	silent_mutation	Average:53.502; most accessible tissue: Minghui63 young leaf, score: 62.741	N	N	N	N
vg1217281529	G -> A	LOC_Os12g29190.1	upstream_gene_variant ; 2277.0bp to feature; MODIFIER	silent_mutation	Average:53.502; most accessible tissue: Minghui63 young leaf, score: 62.741	N	N	N	N
vg1217281529	G -> A	LOC_Os12g29180-LOC_Os12g29190	intergenic_region ; MODIFIER	silent_mutation	Average:53.502; most accessible tissue: Minghui63 young leaf, score: 62.741	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1217281529	NA	8.17E-06	mr1124	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
vg1217281529	NA	3.17E-07	mr1188	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
vg1217281529	NA	8.50E-06	mr1218	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
vg1217281529	NA	1.15E-06	mr1422	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
vg1217281529	NA	2.34E-08	mr1583	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
vg1217281529	2.46E-06	NA	mr1022_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
vg1217281529	9.22E-08	NA	mr1023_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
vg1217281529	2.97E-08	NA	mr1055_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
vg1217281529	8.46E-08	NA	mr1079_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
vg1217281529	1.63E-06	NA	mr1083_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
vg1217281529	9.77E-06	NA	mr1083_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
vg1217281529	7.05E-06	NA	mr1104_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
vg1217281529	5.56E-06	NA	mr1107_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
vg1217281529	3.31E-10	NA	mr1132_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
vg1217281529	5.92E-06	NA	mr1132_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
vg1217281529	5.19E-07	NA	mr1226_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
vg1217281529	4.55E-06	NA	mr1226_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
vg1217281529	9.67E-08	NA	mr1390_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
vg1217281529	2.40E-06	NA	mr1489_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
vg1217281529	2.17E-07	NA	mr1490_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
vg1217281529	NA	3.80E-06	mr1850_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