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Detailed information for vg1213231606:

Variant ID: vg1213231606 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 13231606
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 36. )

Flanking Sequence (100 bp) in Reference Genome:

GGGATCGGTTGAGATCGGCGTCGTGGTGTAAACCGGGAAGACGATTTCGCCGACTTGATTCCACACCAGCATCGTTAAAGCAGGGAGTACTTGGCTGAGG[T/C]
TGGTGTTGACGCTGTTGTCGACGAAGCTGGATGACATAGTAGTAGAACCTTAAGTACCAAGTGCCCCTACCTGGCGCGCAACTGTCGACGGATGGTACCT

Reverse complement sequence

AGGTACCATCCGTCGACAGTTGCGCGCCAGGTAGGGGCACTTGGTACTTAAGGTTCTACTACTATGTCATCCAGCTTCGTCGACAACAGCGTCAACACCA[A/G]
CCTCAGCCAAGTACTCCCTGCTTTAACGATGCTGGTGTGGAATCAAGTCGGCGAAATCGTCTTCCCGGTTTACACCACGACGCCGATCTCAACCGATCCC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	43.00%	17.90%	20.12%	19.00%	NA
All Indica	2759	56.10%	5.50%	24.79%	13.56%	NA
All Japonica	1512	16.90%	44.00%	11.11%	27.98%	NA
Aus	269	39.80%	0.70%	29.00%	30.48%	NA
Indica I	595	35.00%	11.90%	34.12%	18.99%	NA
Indica II	465	34.60%	6.20%	33.98%	25.16%	NA
Indica III	913	81.40%	1.00%	13.69%	3.94%	NA
Indica Intermediate	786	55.60%	5.50%	25.19%	13.74%	NA
Temperate Japonica	767	1.30%	78.60%	2.61%	17.47%	NA
Tropical Japonica	504	38.90%	0.80%	22.22%	38.10%	NA
Japonica Intermediate	241	20.70%	24.10%	14.94%	40.25%	NA
VI/Aromatic	96	86.50%	0.00%	6.25%	7.29%	NA
Intermediate	90	42.20%	27.80%	16.67%	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
vg1213231606	T -> C	LOC_Os12g23390.1	missense_variant ; p.Asn13Ser; MODERATE	nonsynonymous_codon	Average:8.933; most accessible tissue: Minghui63 panicle, score: 20.733	benign	0.838	TOLERATED	0.36
vg1213231606	T -> DEL	LOC_Os12g23390.1	N	frameshift_variant	Average:8.933; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1213231606	4.86E-06	NA	mr1348_2	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