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Detailed information for vg1219246262:

Variant ID: vg1219246262 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 19246262
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACGAGCGAAGTCCTGGTCGCGGTGCCTGGCGTAGAGGTCTCTAGTGCTCGCAATGTGGGGCTGCTGCTCCAAGGGAGCGAAGGTGACCCTAGTACGGGTG[T/C]
GTGGCTGGTACCAGCGTAGGTAGGCCTGGTACGCCTCCTCAGTGTGTGGCTCTCCCTCATGGTCCATGACCTCCTCGGTTGCGAGCAACCAGTCCTCAAC

Reverse complement sequence

GTTGAGGACTGGTTGCTCGCAACCGAGGAGGTCATGGACCATGAGGGAGAGCCACACACTGAGGAGGCGTACCAGGCCTACCTACGCTGGTACCAGCCAC[A/G]
CACCCGTACTAGGGTCACCTTCGCTCCCTTGGAGCAGCAGCCCCACATTGCGAGCACTAGAGACCTCTACGCCAGGCACCGCGACCAGGACTTCGCTCGT

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	49.20%	0.30%	14.33%	36.12%	NA
All Indica	2759	23.40%	0.50%	22.04%	54.08%	NA
All Japonica	1512	96.80%	0.00%	0.40%	2.78%	NA
Aus	269	23.80%	0.70%	18.59%	56.88%	NA
Indica I	595	23.90%	0.50%	22.02%	53.61%	NA
Indica II	465	23.40%	0.00%	23.23%	53.33%	NA
Indica III	913	18.90%	0.50%	21.91%	58.60%	NA
Indica Intermediate	786	28.20%	0.60%	21.50%	49.62%	NA
Temperate Japonica	767	98.40%	0.00%	0.26%	1.30%	NA
Tropical Japonica	504	98.00%	0.00%	0.00%	1.98%	NA
Japonica Intermediate	241	89.20%	0.00%	1.66%	9.13%	NA
VI/Aromatic	96	88.50%	0.00%	5.21%	6.25%	NA
Intermediate	90	75.60%	0.00%	8.89%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1219246262	T -> C	LOC_Os12g31930.1	missense_variant ; p.His137Arg; MODERATE	nonsynonymous_codon ; H137R	Average:7.252; most accessible tissue: Callus, score: 23.247	benign	0.231	TOLERATED	1.00
vg1219246262	T -> DEL	LOC_Os12g31930.1	N	frameshift_variant	Average:7.252; most accessible tissue: Callus, score: 23.247	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1219246262	4.53E-07	4.51E-07	mr1760_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
vg1219246262	7.20E-06	7.20E-06	mr1760_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