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Detailed information for vg1212036957:

Variant ID: vg1212036957 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 12036957
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCAATACACGTCAATATGTCCAAAATTCATGTTTTGCTGCTTGTTGAACTTTTTCATTCCGGTCTAAAACATCGCACCCATGTGTGCCAATATATGCCAA[C/T]
ATTGGCATTAATTGACAAAAGTTCGCCGCGCGAATCACGAAGTGATTTTTAGCCACGAACGCACCCAGTACACTCCAATATGTCCAAAAATCATGTTTTG

Reverse complement sequence

CAAAACATGATTTTTGGACATATTGGAGTGTACTGGGTGCGTTCGTGGCTAAAAATCACTTCGTGATTCGCGCGGCGAACTTTTGTCAATTAATGCCAAT[G/A]
TTGGCATATATTGGCACACATGGGTGCGATGTTTTAGACCGGAATGAAAAAGTTCAACAAGCAGCAAAACATGAATTTTGGACATATTGACGTGTATTGG

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	76.50%	1.10%	4.93%	17.52%	NA
All Indica	2759	66.30%	0.30%	6.27%	27.15%	NA
All Japonica	1512	95.50%	1.30%	0.73%	2.45%	NA
Aus	269	73.60%	4.80%	11.52%	10.04%	NA
Indica I	595	81.30%	0.20%	2.52%	15.97%	NA
Indica II	465	61.10%	0.40%	9.68%	28.82%	NA
Indica III	913	57.70%	0.30%	7.56%	34.39%	NA
Indica Intermediate	786	67.80%	0.40%	5.60%	26.21%	NA
Temperate Japonica	767	95.30%	0.50%	0.52%	3.65%	NA
Tropical Japonica	504	95.00%	3.00%	0.40%	1.59%	NA
Japonica Intermediate	241	97.10%	0.40%	2.07%	0.41%	NA
VI/Aromatic	96	70.80%	5.20%	16.67%	7.29%	NA
Intermediate	90	84.40%	4.40%	2.22%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1212036957	C -> DEL	N	N	silent_mutation	Average:16.553; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N
vg1212036957	C -> T	LOC_Os12g21470-LOC_Os12g21490	intergenic_region ; MODIFIER	silent_mutation	Average:16.553; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1212036957	2.36E-06	2.36E-06	mr1973_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