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Detailed information for vg1216470015:

Variant ID: vg1216470015 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 16470015
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTTAATTTTAGAGGAAAACTGAAGTCGTCAAGTTGAGTACTTTACTATGGCCGTTAATGGTAGTATTATACTACCAGTATAATGGCCCTGTTTAGTTCG[C/T]
GAAAAGAAAATTTTTGGGTGTCATATCGAACGTTTGACCGGAAGTCGGAAAGGGTTTTCGGACACGAATAAAAAAACTAATTTCATCACTCGCATGGAAA

Reverse complement sequence

TTTCCATGCGAGTGATGAAATTAGTTTTTTTATTCGTGTCCGAAAACCCTTTCCGACTTCCGGTCAAACGTTCGATATGACACCCAAAAATTTTCTTTTC[G/A]
CGAACTAAACAGGGCCATTATACTGGTAGTATAATACTACCATTAACGGCCATAGTAAAGTACTCAACTTGACGACTTCAGTTTTCCTCTAAAATTAAAT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	67.30%	18.60%	0.28%	13.86%	NA
All Indica	2759	61.70%	24.80%	0.22%	13.34%	NA
All Japonica	1512	77.50%	11.20%	0.26%	10.98%	NA
Aus	269	72.50%	1.90%	0.37%	25.28%	NA
Indica I	595	84.00%	12.10%	0.00%	3.87%	NA
Indica II	465	86.90%	3.40%	0.43%	9.25%	NA
Indica III	913	30.00%	48.00%	0.11%	21.91%	NA
Indica Intermediate	786	66.70%	20.00%	0.38%	12.98%	NA
Temperate Japonica	767	88.30%	1.60%	0.26%	9.91%	NA
Tropical Japonica	504	63.10%	27.20%	0.20%	9.52%	NA
Japonica Intermediate	241	73.40%	8.70%	0.41%	17.43%	NA
VI/Aromatic	96	44.80%	4.20%	1.04%	50.00%	NA
Intermediate	90	75.60%	17.80%	1.11%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1216470015	C -> DEL	N	N	silent_mutation	Average:33.358; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg1216470015	C -> T	LOC_Os12g27940.1	downstream_gene_variant ; 82.0bp to feature; MODIFIER	silent_mutation	Average:33.358; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg1216470015	C -> T	LOC_Os12g27940-LOC_Os12g27950	intergenic_region ; MODIFIER	silent_mutation	Average:33.358; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1216470015	2.02E-06	NA	mr1017	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
vg1216470015	2.61E-07	NA	mr1055	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
vg1216470015	3.86E-08	NA	mr1132	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
vg1216470015	NA	1.78E-06	mr1305	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
vg1216470015	6.77E-06	NA	mr1390	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
vg1216470015	5.38E-06	NA	mr1490	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
vg1216470015	NA	3.94E-06	mr1586	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
vg1216470015	7.92E-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
vg1216470015	3.74E-06	NA	mr1055_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
vg1216470015	2.68E-06	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
vg1216470015	NA	7.18E-07	mr1092_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
vg1216470015	9.10E-09	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
vg1216470015	NA	6.84E-06	mr1152_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
vg1216470015	1.69E-06	NA	mr1178_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
vg1216470015	1.85E-06	NA	mr1178_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
vg1216470015	NA	1.35E-06	mr1378_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
vg1216470015	6.52E-09	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
vg1216470015	1.05E-06	NA	mr1390_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
vg1216470015	5.15E-09	NA	mr1490_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
vg1216470015	1.65E-06	NA	mr1490_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