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Detailed information for vg1215881162:

Variant ID: vg1215881162 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 15881162
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTGCCCTAGTGTGTGCCTCATGTTTAGGCTGAGGGAGTGGCTTTGTCAATAGATCTGCAACATTCAAATCCGTATGTATTTTGCATATCTTCACATCTC[C/T]
TCTACCCACTATCTCGTGAATGAGGTGATACCGCCGTAAAATGTGTTTGGACTTTTGATGCGATCTATGCTCCTTGGCTTGCACAATGGCACCACTATTA

Reverse complement sequence

TAATAGTGGTGCCATTGTGCAAGCCAAGGAGCATAGATCGCATCAAAAGTCCAAACACATTTTACGGCGGTATCACCTCATTCACGAGATAGTGGGTAGA[G/A]
GAGATGTGAAGATATGCAAAATACATACGGATTTGAATGTTGCAGATCTATTGACAAAGCCACTCCCTCAGCCTAAACATGAGGCACACACTAGGGCAAT

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	43.50%	1.50%	39.59%	15.40%	NA
All Indica	2759	30.90%	0.00%	53.64%	15.44%	NA
All Japonica	1512	64.50%	4.00%	14.29%	17.26%	NA
Aus	269	53.50%	0.00%	35.32%	11.15%	NA
Indica I	595	18.30%	0.00%	55.80%	25.88%	NA
Indica II	465	30.80%	0.00%	46.67%	22.58%	NA
Indica III	913	36.80%	0.00%	59.80%	3.40%	NA
Indica Intermediate	786	33.70%	0.00%	48.98%	17.30%	NA
Temperate Japonica	767	93.60%	0.10%	4.17%	2.09%	NA
Tropical Japonica	504	16.70%	10.90%	29.37%	43.06%	NA
Japonica Intermediate	241	71.80%	1.70%	14.94%	11.62%	NA
VI/Aromatic	96	40.60%	6.20%	47.92%	5.21%	NA
Intermediate	90	52.20%	3.30%	37.78%	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
vg1215881162	C -> DEL	LOC_Os12g27096.1	N	frameshift_variant	Average:12.203; most accessible tissue: Callus, score: 20.94	N	N	N	N
vg1215881162	C -> T	LOC_Os12g27096.1	missense_variant ; p.Gly1705Arg; MODERATE	nonsynonymous_codon ; G1705R	Average:12.203; most accessible tissue: Callus, score: 20.94	unknown	unknown	DELETERIOUS	0.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1215881162	1.56E-06	NA	mr1174	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