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Detailed information for vg0111937994:

Variant ID: vg0111937994 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 11937994
Reference Allele: C	Alternative Allele: G
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.86, C: 0.14, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

CCACCGCTCAACCACGAAGCCACCGCACGCCCCCTTCGTCAAGGGGTGGGCAAGGCGAGAGCCGGCCCACAGAGAGGACTACCCAAGCCTCGATCACTAG[C/G]
GTAGTTCTTCCTTCACTCCGAAGGTGGTGAACTCCAAACCACTCACAAACCGGCGCCGGGCCTCTTCCATAATCTTCTCGGAGAGGTCACTGGGCAACTC

Reverse complement sequence

GAGTTGCCCAGTGACCTCTCCGAGAAGATTATGGAAGAGGCCCGGCGCCGGTTTGTGAGTGGTTTGGAGTTCACCACCTTCGGAGTGAAGGAAGAACTAC[G/C]
CTAGTGATCGAGGCTTGGGTAGTCCTCTCTGTGGGCCGGCTCTCGCCTTGCCCACCCCTTGACGAAGGGGGCGTGCGGTGGCTTCGTGGTTGAGCGGTGG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	71.60%	22.20%	5.56%	0.72%	NA
All Indica	2759	91.30%	1.30%	7.21%	0.18%	NA
All Japonica	1512	33.60%	64.00%	0.46%	1.92%	NA
Aus	269	84.80%	0.70%	14.50%	0.00%	NA
Indica I	595	92.60%	0.70%	6.55%	0.17%	NA
Indica II	465	90.80%	2.60%	6.24%	0.43%	NA
Indica III	913	93.30%	0.40%	6.24%	0.00%	NA
Indica Intermediate	786	88.30%	2.00%	9.41%	0.25%	NA
Temperate Japonica	767	27.90%	72.00%	0.13%	0.00%	NA
Tropical Japonica	504	47.20%	45.80%	1.19%	5.75%	NA
Japonica Intermediate	241	23.20%	76.80%	0.00%	0.00%	NA
VI/Aromatic	96	66.70%	21.90%	11.46%	0.00%	NA
Intermediate	90	70.00%	22.20%	7.78%	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
vg0111937994	C -> G	LOC_Os01g21360.1	upstream_gene_variant ; 509.0bp to feature; MODIFIER	silent_mutation	Average:39.612; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0111937994	C -> G	LOC_Os01g21360-LOC_Os01g21380	intergenic_region ; MODIFIER	silent_mutation	Average:39.612; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0111937994	C -> DEL	N	N	silent_mutation	Average:39.612; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0111937994	NA	6.56E-12	Plant_height	Jap_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
vg0111937994	NA	1.72E-07	mr1040	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
vg0111937994	NA	2.31E-16	mr1156	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
vg0111937994	NA	7.13E-08	mr1162	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
vg0111937994	NA	3.13E-07	mr1164	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
vg0111937994	NA	9.34E-06	mr1263	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
vg0111937994	NA	9.34E-06	mr1451	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
vg0111937994	NA	7.68E-09	mr1624	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
vg0111937994	NA	5.91E-08	mr1648	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
vg0111937994	NA	5.35E-17	mr1740	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
vg0111937994	NA	4.75E-06	mr1740	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
vg0111937994	NA	2.79E-12	mr1741	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
vg0111937994	NA	1.29E-20	mr1010_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
vg0111937994	NA	2.13E-07	mr1030_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
vg0111937994	NA	7.84E-06	mr1053_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
vg0111937994	NA	1.14E-09	mr1164_2	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
vg0111937994	NA	3.39E-08	mr1576_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
vg0111937994	NA	8.47E-09	mr1624_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
vg0111937994	NA	1.19E-09	mr1709_2	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