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Detailed information for vg1218161219:

Variant ID: vg1218161219 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 18161219
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

CATCCCTCTTATTGCCGATGACAATATTTTTAAGCTTTATATCTAATTCTTCCTCGACTTTTCGTTGTGTTGCAGCTCTTCGCACGGATATCGTGACGCA[G/A]
CGGGTCAAGGATGTACTTATCAGTCCTGCTTCCATAGCCGAGGAGGTGCCGACCCCGCTCTGCGACAAGCCAGCGGCCGCCATCAATGTGCGTGAGAAAA

Reverse complement sequence

TTTTCTCACGCACATTGATGGCGGCCGCTGGCTTGTCGCAGAGCGGGGTCGGCACCTCCTCGGCTATGGAAGCAGGACTGATAAGTACATCCTTGACCCG[C/T]
TGCGTCACGATATCCGTGCGAAGAGCTGCAACACAACGAAAAGTCGAGGAAGAATTAGATATAAAGCTTAAAAATATTGTCATCGGCAATAAGAGGGATG

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	64.90%	9.50%	3.07%	22.60%	NA
All Indica	2759	63.20%	0.60%	1.38%	34.76%	NA
All Japonica	1512	65.70%	27.50%	6.48%	0.33%	NA
Aus	269	67.30%	0.00%	0.37%	32.34%	NA
Indica I	595	91.80%	0.30%	0.67%	7.23%	NA
Indica II	465	54.20%	0.40%	1.51%	43.87%	NA
Indica III	913	52.00%	0.70%	1.42%	45.89%	NA
Indica Intermediate	786	60.10%	0.90%	1.78%	37.28%	NA
Temperate Japonica	767	84.40%	6.50%	8.60%	0.52%	NA
Tropical Japonica	504	35.10%	62.10%	2.78%	0.00%	NA
Japonica Intermediate	241	70.10%	22.00%	7.47%	0.41%	NA
VI/Aromatic	96	91.70%	0.00%	0.00%	8.33%	NA
Intermediate	90	64.40%	16.70%	8.89%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1218161219	G -> DEL	LOC_Os12g30270.1	N	frameshift_variant	Average:49.235; most accessible tissue: Zhenshan97 young leaf, score: 78.044	N	N	N	N
vg1218161219	G -> A	LOC_Os12g30270.1	synonymous_variant ; p.Gln43Gln; LOW	synonymous_codon	Average:49.235; most accessible tissue: Zhenshan97 young leaf, score: 78.044	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1218161219	8.14E-06	NA	Awn_length	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1218161219	NA	3.57E-08	mr1124	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
vg1218161219	NA	3.22E-06	mr1157	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
vg1218161219	4.69E-07	NA	mr1201	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
vg1218161219	4.64E-06	NA	mr1201	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
vg1218161219	NA	1.68E-06	mr1206	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
vg1218161219	3.12E-06	NA	mr1219	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
vg1218161219	NA	5.82E-07	mr1338	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
vg1218161219	NA	1.61E-06	mr1446	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
vg1218161219	NA	1.26E-11	mr1454	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
vg1218161219	NA	1.55E-07	mr1668	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
vg1218161219	NA	1.03E-07	mr1779	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
vg1218161219	NA	8.89E-06	mr1786	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
vg1218161219	NA	4.10E-06	mr1743_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
vg1218161219	NA	4.14E-10	mr1905_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