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Detailed information for vg1226816492:

Variant ID: vg1226816492 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 26816492
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:

CTGCGAGGTCTCCGATTGCGTAGCGGGCCAACTGAGTGAACCGGTTCAGATATTCTTGCACCGTTGTGTTTCCTTGTCGCAGCCTTCTGAACTCGTTCTT[C/G]
TTCATGCGCATCACCGCGGCAGGCACGAAGTTCTCACGAAAAGCTGCAGTGAATTCTTCCCAAGTGGGTTCTCCAGCATCTTCTTCTCGAGCTTCCTTGT

Reverse complement sequence

ACAAGGAAGCTCGAGAAGAAGATGCTGGAGAACCCACTTGGGAAGAATTCACTGCAGCTTTTCGTGAGAACTTCGTGCCTGCCGCGGTGATGCGCATGAA[G/C]
AAGAACGAGTTCAGAAGGCTGCGACAAGGAAACACAACGGTGCAAGAATATCTGAACCGGTTCACTCAGTTGGCCCGCTACGCAATCGGAGACCTCGCAG

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	89.20%	9.80%	0.97%	0.06%	NA
All Indica	2759	89.50%	9.50%	0.87%	0.11%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	20.40%	71.70%	7.81%	0.00%	NA
Indica I	595	96.50%	3.00%	0.50%	0.00%	NA
Indica II	465	81.70%	17.00%	1.29%	0.00%	NA
Indica III	913	92.20%	7.00%	0.44%	0.33%	NA
Indica Intermediate	786	85.60%	13.00%	1.40%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	94.80%	4.20%	1.04%	0.00%	NA
Intermediate	90	96.70%	3.30%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1226816492	C -> DEL	LOC_Os12g43179.1	N	frameshift_variant	Average:47.901; most accessible tissue: Zhenshan97 flag leaf, score: 81.605	N	N	N	N
vg1226816492	C -> G	LOC_Os12g43179.1	missense_variant ; p.Lys378Asn; MODERATE	nonsynonymous_codon ; K378N	Average:47.901; most accessible tissue: Zhenshan97 flag leaf, score: 81.605	unknown	unknown	DELETERIOUS	0.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1226816492	NA	5.93E-14	mr1317	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
vg1226816492	NA	2.55E-09	mr1317	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
vg1226816492	NA	1.11E-08	mr1608	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
vg1226816492	NA	6.12E-06	mr1649	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
vg1226816492	NA	6.52E-06	mr1818	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
vg1226816492	2.98E-08	7.06E-47	mr1855	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
vg1226816492	2.32E-06	1.23E-20	mr1855	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
vg1226816492	NA	8.52E-13	mr1897	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
vg1226816492	NA	1.08E-11	mr1927	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
vg1226816492	NA	2.59E-16	mr1317_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
vg1226816492	NA	5.12E-11	mr1317_2	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
vg1226816492	NA	3.72E-09	mr1608_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
vg1226816492	NA	2.84E-06	mr1608_2	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
vg1226816492	NA	3.00E-13	mr1610_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
vg1226816492	NA	4.29E-07	mr1610_2	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
vg1226816492	6.38E-06	1.29E-19	mr1818_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
vg1226816492	NA	1.78E-10	mr1818_2	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
vg1226816492	1.76E-09	1.01E-51	mr1855_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
vg1226816492	1.64E-07	1.91E-20	mr1855_2	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
vg1226816492	NA	3.22E-15	mr1897_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
vg1226816492	NA	7.48E-07	mr1897_2	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
vg1226816492	NA	1.67E-19	mr1914_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
vg1226816492	NA	2.51E-12	mr1914_2	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
vg1226816492	NA	1.92E-22	mr1927_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
vg1226816492	NA	1.88E-10	mr1927_2	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