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Detailed information for vg1204296378:

Variant ID: vg1204296378 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 4296378
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCGTTCTCCCATCCTAACGACGAACCTACTTAGCGCCACCATGCATCCGGTTAGCTTCTGTACTTCCTTGAGTCTAGTGGGCGACTTCATGTTCTCGATT[T/A]
CCTTGATCTTCTCGGGATTTGCTTCTATTCCTCTGCCAGAGACGAGGAATCCGAGCAGTTTGCCTGACGGTACCCCGAACATGCACTTCTCAGGATTGAG

Reverse complement sequence

CTCAATCCTGAGAAGTGCATGTTCGGGGTACCGTCAGGCAAACTGCTCGGATTCCTCGTCTCTGGCAGAGGAATAGAAGCAAATCCCGAGAAGATCAAGG[A/T]
AATCGAGAACATGAAGTCGCCCACTAGACTCAAGGAAGTACAGAAGCTAACCGGATGCATGGTGGCGCTAAGTAGGTTCGTCGTTAGGATGGGAGAACGA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	23.80%	1.00%	0.74%	74.42%	NA
All Indica	2759	6.00%	0.90%	0.65%	92.39%	NA
All Japonica	1512	55.80%	0.00%	0.13%	44.05%	NA
Aus	269	25.70%	7.80%	3.72%	62.83%	NA
Indica I	595	7.10%	0.20%	0.67%	92.10%	NA
Indica II	465	7.30%	0.90%	1.08%	90.75%	NA
Indica III	913	1.50%	1.40%	0.22%	96.82%	NA
Indica Intermediate	786	9.70%	1.00%	0.89%	88.42%	NA
Temperate Japonica	767	80.30%	0.00%	0.13%	19.56%	NA
Tropical Japonica	504	28.00%	0.00%	0.00%	72.02%	NA
Japonica Intermediate	241	36.10%	0.00%	0.41%	63.49%	NA
VI/Aromatic	96	14.60%	1.00%	4.17%	80.21%	NA
Intermediate	90	36.70%	0.00%	1.11%	62.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1204296378	T -> DEL	LOC_Os12g08450.1	N	frameshift_variant	Average:9.265; most accessible tissue: Callus, score: 25.675	N	N	N	N
vg1204296378	T -> A	LOC_Os12g08450.1	missense_variant ; p.Glu118Val; MODERATE	nonsynonymous_codon ; E118V	Average:9.265; most accessible tissue: Callus, score: 25.675	unknown	unknown	DELETERIOUS	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1204296378	6.65E-08	NA	mr1718_2	Ind_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