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Detailed information for vg1213231314:

Variant ID: vg1213231314 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 13231314
Reference Allele: A	Alternative Allele: C
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.87, A: 0.13, others allele: 0.00, population size: 32. )

Flanking Sequence (100 bp) in Reference Genome:

GCTGAATCCCACGCTCTTTGCAGGCGCGAATTTCAGCGCGGACATTGAGGAAAACCCAGCAGGCTTGCAAAGTGTGTTTCTTGGTTTTGTGGATAGGACA[A/C]
CAGGACCTTGTGGCTTCGGAAGTCATCTTTGTCGGCTCGCGGTTTATGTCGGAAGGACAAGGTTTGGCCACATCAGAATCCTTCTCGAGCTCGGATGTCG

Reverse complement sequence

CGACATCCGAGCTCGAGAAGGATTCTGATGTGGCCAAACCTTGTCCTTCCGACATAAACCGCGAGCCGACAAAGATGACTTCCGAAGCCACAAGGTCCTG[T/G]
TGTCCTATCCACAAAACCAAGAAACACACTTTGCAAGCCTGCTGGGTTTTCCTCAATGTCCGCGCTGAAATTCGCGCCTGCAAAGAGCGTGGGATTCAGC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	47.70%	17.40%	18.62%	16.27%	NA
All Indica	2759	69.20%	4.60%	22.94%	3.30%	NA
All Japonica	1512	6.50%	44.00%	7.28%	42.20%	NA
Aus	269	60.60%	1.90%	28.62%	8.92%	NA
Indica I	595	58.00%	7.60%	30.76%	3.70%	NA
Indica II	465	67.30%	5.80%	18.28%	8.60%	NA
Indica III	913	76.90%	2.00%	21.14%	0.00%	NA
Indica Intermediate	786	69.80%	4.60%	21.88%	3.69%	NA
Temperate Japonica	767	1.40%	78.50%	1.83%	18.25%	NA
Tropical Japonica	504	14.30%	1.00%	11.71%	73.02%	NA
Japonica Intermediate	241	6.60%	24.10%	15.35%	53.94%	NA
VI/Aromatic	96	51.00%	0.00%	47.92%	1.04%	NA
Intermediate	90	40.00%	27.80%	15.56%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1213231314	A -> C	LOC_Os12g23390.1	missense_variant ; p.Cys110Trp; MODERATE	stop_gained	Average:13.419; most accessible tissue: Callus, score: 36.349	N	N	N	N
vg1213231314	A -> C	LOC_Os12g23390.1	missense_variant ; p.Cys110Trp; MODERATE	nonsynonymous_codon ; C110W	Average:13.419; most accessible tissue: Callus, score: 36.349	unknown	unknown	TOLERATED	1.00
vg1213231314	A -> DEL	LOC_Os12g23390.1	N	frameshift_variant	Average:13.419; most accessible tissue: Callus, score: 36.349	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1213231314	NA	2.00E-08	mr1022	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
vg1213231314	NA	1.25E-13	mr1079	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
vg1213231314	NA	1.40E-11	mr1178	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
vg1213231314	NA	1.74E-07	mr1657	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
vg1213231314	NA	1.37E-13	mr1079_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
vg1213231314	NA	7.46E-08	mr1156_2	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
vg1213231314	NA	3.14E-08	mr1607_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