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Detailed information for vg1208212432:

Variant ID: vg1208212432 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 8212432
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATCCTCTAGTCTCTCTCTGTCCTGCTGCTTCATTTATCGCCAAAATCTAATCTTTAAAATGTTGCTTTTCTCTTTTGTCTTTTTGTTTGTAGATGGCCG[G/A]
CAGCATCAACCGTCGTGGTCTGGACCTGACTAGCTTCGTTTTGGAGCTGCGGGGCATGTGCGTTGTCCTGGGGTATCCGCATGGAGTGGATTACCAGGGC

Reverse complement sequence

GCCCTGGTAATCCACTCCATGCGGATACCCCAGGACAACGCACATGCCCCGCAGCTCCAAAACGAAGCTAGTCAGGTCCAGACCACGACGGTTGATGCTG[C/T]
CGGCCATCTACAAACAAAAAGACAAAAGAGAAAAGCAACATTTTAAAGATTAGATTTTGGCGATAAATGAAGCAGCAGGACAGAGAGAGACTAGAGGATT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	40.70%	0.70%	27.25%	31.36%	NA
All Indica	2759	28.30%	0.90%	34.76%	35.96%	NA
All Japonica	1512	52.10%	0.30%	16.93%	30.69%	NA
Aus	269	80.30%	0.00%	18.96%	0.74%	NA
Indica I	595	23.00%	0.50%	29.24%	47.23%	NA
Indica II	465	31.80%	0.60%	20.65%	46.88%	NA
Indica III	913	29.20%	1.10%	48.41%	21.25%	NA
Indica Intermediate	786	29.30%	1.30%	31.42%	38.04%	NA
Temperate Japonica	767	75.90%	0.00%	4.04%	20.08%	NA
Tropical Japonica	504	22.00%	0.60%	38.10%	39.29%	NA
Japonica Intermediate	241	39.40%	0.40%	13.69%	46.47%	NA
VI/Aromatic	96	88.50%	0.00%	5.21%	6.25%	NA
Intermediate	90	57.80%	3.30%	18.89%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1208212432	G -> DEL	LOC_Os12g14400.1	N	frameshift_variant	Average:20.199; most accessible tissue: Callus, score: 28.638	N	N	N	N
vg1208212432	G -> A	LOC_Os12g14400.1	missense_variant ; p.Gly73Asp; MODERATE	nonsynonymous_codon ; G73D	Average:20.199; most accessible tissue: Callus, score: 28.638	unknown	unknown	TOLERATED	0.08

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1208212432	3.08E-06	3.08E-06	mr1068	Jap_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
vg1208212432	NA	6.44E-08	mr1090	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
vg1208212432	NA	2.16E-06	mr1211	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
vg1208212432	NA	3.03E-07	mr1090_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
vg1208212432	NA	8.05E-07	mr1211_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