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Detailed information for vg1107901260:

Variant ID: vg1107901260 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 7901260
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:

CATTGGTGCACCAACAAAGTGGAAATTTTCTGGCAGCTGACTTGCATTATGATAGTTCACAAATGGATGTGTCTGGGTAAATGGAGAGATCTTATTACTC[T/C]
GTAAATAATTTAGGAAACCACCTGGTGGATACATCTTGAAAAAGAAAACAACAAAAAAAATTAATATCTGTGTCAAGAACAGAAGTGGTGAAATACAAGC

Reverse complement sequence

GCTTGTATTTCACCACTTCTGTTCTTGACACAGATATTAATTTTTTTTGTTGTTTTCTTTTTCAAGATGTATCCACCAGGTGGTTTCCTAAATTATTTAC[A/G]
GAGTAATAAGATCTCTCCATTTACCCAGACACATCCATTTGTGAACTATCATAATGCAAGTCAGCTGCCAGAAAATTTCCACTTTGTTGGTGCACCAATG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	86.80%	10.30%	2.96%	0.00%	NA
All Indica	2759	99.10%	0.50%	0.47%	0.00%	NA
All Japonica	1512	62.80%	29.40%	7.80%	0.00%	NA
Aus	269	97.40%	0.00%	2.60%	0.00%	NA
Indica I	595	99.70%	0.00%	0.34%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.70%	0.30%	0.00%	0.00%	NA
Indica Intermediate	786	97.30%	1.30%	1.40%	0.00%	NA
Temperate Japonica	767	83.20%	6.90%	9.91%	0.00%	NA
Tropical Japonica	504	35.50%	60.70%	3.77%	0.00%	NA
Japonica Intermediate	241	54.80%	35.70%	9.54%	0.00%	NA
VI/Aromatic	96	86.50%	13.50%	0.00%	0.00%	NA
Intermediate	90	82.20%	15.60%	2.22%	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
vg1107901260	T -> C	LOC_Os11g14160.1	missense_variant ; p.Gln70Arg; MODERATE	nonsynonymous_codon ; Q70R	Average:64.98; most accessible tissue: Minghui63 root, score: 80.163	unknown	unknown	TOLERATED	0.10

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1107901260	NA	2.21E-06	mr1248	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
vg1107901260	NA	2.16E-06	mr1269	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
vg1107901260	NA	1.14E-06	mr1315	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
vg1107901260	NA	3.61E-06	mr1418	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
vg1107901260	NA	1.08E-06	mr1420	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
vg1107901260	NA	6.62E-10	mr1506	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
vg1107901260	4.23E-06	4.23E-06	mr1506	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
vg1107901260	4.44E-06	4.46E-08	mr1543	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
vg1107901260	NA	6.37E-08	mr1543	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
vg1107901260	NA	2.69E-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
vg1107901260	NA	9.55E-08	mr1677	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
vg1107901260	NA	4.39E-07	mr1797	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
vg1107901260	NA	4.39E-07	mr1801	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
vg1107901260	NA	5.45E-14	mr1871	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
vg1107901260	NA	3.50E-07	mr1886	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
vg1107901260	NA	6.16E-09	mr1979	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
vg1107901260	NA	2.37E-06	mr1369_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
vg1107901260	NA	5.09E-07	mr1453_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
vg1107901260	NA	7.85E-11	mr1680_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
vg1107901260	NA	2.01E-21	mr1871_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