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Detailed information for vg1223355966:

Variant ID: vg1223355966 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 23355966
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAAGCCGCCATTTTCCACTGGTGTACAGACATCTTTCCAGGCTACAAGGCAATGTTCAATGTTCACCACTCACCTCCTGCTGTCCCTTCCAAAGAAATCC[C/T]
CGACATTTCCGCTCGATGTCCTTGATTGCCCACTTTGGAAGTTGCAATACAGACATGAAGTGAACTGGGAGGGCCATGAGAACGGATTTAATCAAGCAGA

Reverse complement sequence

TCTGCTTGATTAAATCCGTTCTCATGGCCCTCCCAGTTCACTTCATGTCTGTATTGCAACTTCCAAAGTGGGCAATCAAGGACATCGAGCGGAAATGTCG[G/A]
GGATTTCTTTGGAAGGGACAGCAGGAGGTGAGTGGTGAACATTGAACATTGCCTTGTAGCCTGGAAAGATGTCTGTACACCAGTGGAAAATGGCGGCTTG

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	59.40%	2.70%	7.17%	30.77%	NA
All Indica	2759	45.60%	0.20%	2.86%	51.40%	NA
All Japonica	1512	79.00%	6.80%	13.89%	0.33%	NA
Aus	269	71.00%	6.30%	17.47%	5.20%	NA
Indica I	595	17.80%	0.20%	2.35%	79.66%	NA
Indica II	465	82.60%	0.00%	1.94%	15.48%	NA
Indica III	913	41.60%	0.10%	2.08%	56.19%	NA
Indica Intermediate	786	49.20%	0.40%	4.71%	45.67%	NA
Temperate Japonica	767	90.70%	2.10%	7.17%	0.00%	NA
Tropical Japonica	504	75.20%	6.90%	17.06%	0.79%	NA
Japonica Intermediate	241	49.40%	21.60%	28.63%	0.41%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	75.60%	3.30%	3.33%	17.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1223355966	C -> DEL	LOC_Os12g38020.1	N	frameshift_variant	Average:8.899; most accessible tissue: Callus, score: 36.638	N	N	N	N
vg1223355966	C -> T	LOC_Os12g38020.1	synonymous_variant ; p.Arg1099Arg; LOW	synonymous_codon	Average:8.899; most accessible tissue: Callus, score: 36.638	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1223355966	3.33E-07	1.02E-10	mr1057	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
vg1223355966	NA	5.20E-07	mr1057_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