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Detailed information for vg1216118354:

Variant ID: vg1216118354 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 16118354
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTAGGAATATGTGGAGTAGCATGACTAACAGTATTAACAGGTGATGAATAATAATTAAAATCAGTACTGCTAGTCGTGGTATGAAAACCTAGAGAAATT[T/C]
CCAGGGAACCGGTCTGACCGGCCAAGCATCCGGTCTGATCGGCCCTTGGCCCGGTCTGACTGGTGGTCAGTGGTGCGGTCAGACCGGTTACAGGAGGCCT

Reverse complement sequence

AGGCCTCCTGTAACCGGTCTGACCGCACCACTGACCACCAGTCAGACCGGGCCAAGGGCCGATCAGACCGGATGCTTGGCCGGTCAGACCGGTTCCCTGG[A/G]
AATTTCTCTAGGTTTTCATACCACGACTAGCAGTACTGATTTTAATTATTATTCATCACCTGTTAATACTGTTAGTCATGCTACTCCACATATTCCTAAT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	32.00%	0.10%	1.33%	66.59%	NA
All Indica	2759	11.20%	0.00%	1.92%	86.81%	NA
All Japonica	1512	65.50%	0.30%	0.46%	33.73%	NA
Aus	269	30.50%	0.00%	0.37%	69.14%	NA
Indica I	595	13.90%	0.00%	0.67%	85.38%	NA
Indica II	465	11.40%	0.20%	2.37%	86.02%	NA
Indica III	913	6.50%	0.00%	2.85%	90.69%	NA
Indica Intermediate	786	14.60%	0.00%	1.53%	83.84%	NA
Temperate Japonica	767	95.70%	0.00%	0.00%	4.30%	NA
Tropical Japonica	504	15.10%	0.80%	1.19%	82.94%	NA
Japonica Intermediate	241	75.10%	0.00%	0.41%	24.48%	NA
VI/Aromatic	96	82.30%	0.00%	0.00%	17.71%	NA
Intermediate	90	54.40%	0.00%	2.22%	43.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1216118354	T -> C	LOC_Os12g27390-LOC_Os12g27400	intergenic_region ; MODIFIER	silent_mutation	Average:13.897; most accessible tissue: Callus, score: 36.78	N	N	N	N
vg1216118354	T -> DEL	N	N	silent_mutation	Average:13.897; most accessible tissue: Callus, score: 36.78	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1216118354	NA	4.02E-06	mr1076	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
vg1216118354	NA	1.49E-07	mr1083	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
vg1216118354	4.78E-06	4.78E-06	mr1362	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
vg1216118354	NA	8.10E-06	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