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Detailed information for vg1220380232:

Variant ID: vg1220380232 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 20380232
Reference Allele: G	Alternative Allele: C
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GACTCGTAGTTCCACAATTCATTCATGCTAGCTACCGATTTGAAGCTCAGCCACGTGACGCCCGACGACGATGACGTCGACGGCGAGATCTTGTTGTTGT[G/C]
GTCGAGCTGCCCGCGCGCGCGCGGGGCTCGGGAGGCTTTGTTGGCGAAATAACCCCGATCAAACACCTTACGTGCAAACTGCAGCTGTCCGGCACGGCAA

Reverse complement sequence

TTGCCGTGCCGGACAGCTGCAGTTTGCACGTAAGGTGTTTGATCGGGGTTATTTCGCCAACAAAGCCTCCCGAGCCCCGCGCGCGCGCGGGCAGCTCGAC[C/G]
ACAACAACAAGATCTCGCCGTCGACGTCATCGTCGTCGGGCGTCACGTGGCTGAGCTTCAAATCGGTAGCTAGCATGAATGAATTGTGGAACTACGAGTC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	55.50%	28.20%	0.55%	15.74%	NA
All Indica	2759	80.50%	9.20%	0.40%	9.86%	NA
All Japonica	1512	6.00%	67.30%	0.46%	26.32%	NA
Aus	269	90.30%	8.20%	1.12%	0.37%	NA
Indica I	595	56.60%	24.90%	1.18%	17.31%	NA
Indica II	465	91.00%	7.50%	0.00%	1.51%	NA
Indica III	913	87.20%	1.10%	0.00%	11.72%	NA
Indica Intermediate	786	84.70%	7.80%	0.51%	7.00%	NA
Temperate Japonica	767	1.80%	94.00%	0.00%	4.17%	NA
Tropical Japonica	504	6.70%	28.00%	1.19%	64.09%	NA
Japonica Intermediate	241	17.40%	64.30%	0.41%	17.84%	NA
VI/Aromatic	96	25.00%	8.30%	3.12%	63.54%	NA
Intermediate	90	47.80%	36.70%	2.22%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1220380232	G -> C	LOC_Os12g33780.1	downstream_gene_variant ; 2975.0bp to feature; MODIFIER	silent_mutation	Average:52.961; most accessible tissue: Callus, score: 86.663	N	N	N	N
vg1220380232	G -> C	LOC_Os12g33780-LOC_Os12g33800	intergenic_region ; MODIFIER	silent_mutation	Average:52.961; most accessible tissue: Callus, score: 86.663	N	N	N	N
vg1220380232	G -> DEL	N	N	silent_mutation	Average:52.961; most accessible tissue: Callus, score: 86.663	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1220380232	4.11E-11	1.17E-86	mr1334	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
vg1220380232	4.32E-06	1.31E-08	mr1334	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
vg1220380232	3.99E-15	3.60E-97	mr1334_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
vg1220380232	6.43E-09	7.72E-12	mr1334_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
vg1220380232	2.41E-08	2.95E-55	mr1991_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
vg1220380232	NA	4.70E-07	mr1991_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