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Detailed information for vg1217708036:

Variant ID: vg1217708036 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 17708036
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, C: 0.03, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:

AGTGAAATATGGGGAAGAAGAGAGAGTAGTAGAGAGATTGAAGTGCTTGTTACCTTGGTGCAAGCTAGGCCTTTACAATTGGGATAGTTCCTTGAAGCTT[C/G]
CGGCACTGCCTTTTTAGCTCCTCGTTGCGACAGTAACGGACGTCTATTTCTCGGAGTGTAGTTGGTAGGCGGTCTTTGGGCAGTGAGCGGATGGTTGTGC

Reverse complement sequence

GCACAACCATCCGCTCACTGCCCAAAGACCGCCTACCAACTACACTCCGAGAAATAGACGTCCGTTACTGTCGCAACGAGGAGCTAAAAAGGCAGTGCCG[G/C]
AAGCTTCAAGGAACTATCCCAATTGTAAAGGCCTAGCTTGCACCAAGGTAACAAGCACTTCAATCTCTCTACTACTCTCTCTTCTTCCCCATATTTCACT

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	23.60%	17.30%	18.45%	40.61%	NA
All Indica	2759	9.00%	16.40%	27.04%	47.52%	NA
All Japonica	1512	44.60%	19.60%	5.36%	30.42%	NA
Aus	269	51.70%	8.60%	8.18%	31.60%	NA
Indica I	595	8.90%	28.20%	27.23%	35.63%	NA
Indica II	465	14.00%	3.70%	22.37%	60.00%	NA
Indica III	913	3.70%	13.60%	29.90%	52.79%	NA
Indica Intermediate	786	12.30%	18.30%	26.34%	43.00%	NA
Temperate Japonica	767	76.10%	11.60%	7.56%	4.69%	NA
Tropical Japonica	504	4.20%	33.70%	2.58%	59.52%	NA
Japonica Intermediate	241	28.60%	15.80%	4.15%	51.45%	NA
VI/Aromatic	96	21.90%	29.20%	11.46%	37.50%	NA
Intermediate	90	37.80%	18.90%	13.33%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1217708036	C -> DEL	LOC_Os12g29690.1	N	frameshift_variant	Average:26.887; most accessible tissue: Zhenshan97 root, score: 55.432	N	N	N	N
vg1217708036	C -> G	LOC_Os12g29690.1	synonymous_variant ; p.Arg1493Arg; LOW	synonymous_codon	Average:26.887; most accessible tissue: Zhenshan97 root, score: 55.432	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1217708036	4.75E-06	4.75E-06	mr1260_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