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Detailed information for vg1204380405:

Variant ID: vg1204380405 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 4380405
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TATCCCGAAGTGTTCCTTGAAGACCTCACTACCATGCCACCCAAGAGAGAACTTGAATTCCGGATTGATTTGGCACCAGGAACTGCCCCAATTTACAAGA[A/G]
ACCGTACAGAATGGCAACCAACAAGCTAGCACAGGTCAAGAAGCAGGTTGATGAGCAGCTGCAGAAAGGGTACATTCGACCAAGTACTTTACCTTGGGGT

Reverse complement sequence

ACCCCAAGGTAAAGTACTTGGTCGAATGTACCCTTTCTGCAGCTGCTCATCAACCTGCTTCTTGACCTGTGCTAGCTTGTTGGTTGCCATTCTGTACGGT[T/C]
TCTTGTAAATTGGGGCAGTTCCTGGTGCCAAATCAATCCGGAATTCAAGTTCTCTCTTGGGTGGCATGGTAGTGAGGTCTTCAAGGAACACTTCGGGATA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	31.00%	0.30%	0.47%	68.20%	NA
All Indica	2759	19.00%	0.10%	0.33%	80.65%	NA
All Japonica	1512	55.00%	0.30%	0.46%	44.25%	NA
Aus	269	23.40%	2.20%	1.49%	72.86%	NA
Indica I	595	32.10%	0.00%	1.01%	66.89%	NA
Indica II	465	27.70%	0.00%	0.22%	72.04%	NA
Indica III	913	2.50%	0.10%	0.00%	97.37%	NA
Indica Intermediate	786	22.90%	0.10%	0.25%	76.72%	NA
Temperate Japonica	767	80.20%	0.40%	0.65%	18.77%	NA
Tropical Japonica	504	26.60%	0.20%	0.20%	73.02%	NA
Japonica Intermediate	241	34.00%	0.40%	0.41%	65.15%	NA
VI/Aromatic	96	15.60%	0.00%	0.00%	84.38%	NA
Intermediate	90	38.90%	1.10%	2.22%	57.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1204380405	A -> DEL	LOC_Os12g08620.1	N	frameshift_variant	Average:14.01; most accessible tissue: Callus, score: 47.216	N	N	N	N
vg1204380405	A -> G	LOC_Os12g08620.1	missense_variant ; p.Lys479Arg; MODERATE	nonsynonymous_codon ; K479R	Average:14.01; most accessible tissue: Callus, score: 47.216	unknown	unknown	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1204380405	NA	2.19E-11	mr1361_2	Jap_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
vg1204380405	4.71E-07	8.32E-07	mr1578_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
vg1204380405	NA	8.46E-06	mr1853_2	Jap_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