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Detailed information for vg0112179197:

Variant ID: vg0112179197 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 12179197
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, T: 0.07, others allele: 0.00, population size: 85. )

Flanking Sequence (100 bp) in Reference Genome:

AACAGTTAGATAGGCTACCCCAAATATTGTACTGGTGTGATTATGGTGACACTACAAGGAATCTGTTAATGCGTGATGAAAAAATTCCGTCACGGATCAT[C/T]
AAAAAACCGTCACTATGCAGCACCTGTGATGGTTTCAGAGATGGTCACGGATTGAGCGTCATGGATTAACCTCTGTGACGGTTTACCAAAAACCATCACG

Reverse complement sequence

CGTGATGGTTTTTGGTAAACCGTCACAGAGGTTAATCCATGACGCTCAATCCGTGACCATCTCTGAAACCATCACAGGTGCTGCATAGTGACGGTTTTTT[G/A]
ATGATCCGTGACGGAATTTTTTCATCACGCATTAACAGATTCCTTGTAGTGTCACCATAATCACACCAGTACAATATTTGGGGTAGCCTATCTAACTGTT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	11.20%	5.60%	5.73%	77.44%	NA
All Indica	2759	0.90%	0.50%	8.23%	90.36%	NA
All Japonica	1512	32.30%	15.70%	2.65%	49.40%	NA
Aus	269	0.70%	0.40%	1.49%	97.40%	NA
Indica I	595	0.70%	0.00%	1.68%	97.65%	NA
Indica II	465	1.50%	1.10%	4.52%	92.90%	NA
Indica III	913	0.30%	0.20%	16.65%	82.80%	NA
Indica Intermediate	786	1.30%	1.00%	5.60%	92.11%	NA
Temperate Japonica	767	52.70%	5.70%	2.35%	39.24%	NA
Tropical Japonica	504	1.00%	33.30%	3.37%	62.30%	NA
Japonica Intermediate	241	32.80%	10.40%	2.07%	54.77%	NA
VI/Aromatic	96	0.00%	1.00%	0.00%	98.96%	NA
Intermediate	90	17.80%	12.20%	0.00%	70.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0112179197	C -> T	LOC_Os01g21700.1	downstream_gene_variant ; 2471.0bp to feature; MODIFIER	silent_mutation	Average:21.118; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0112179197	C -> T	LOC_Os01g21700-LOC_Os01g21710	intergenic_region ; MODIFIER	silent_mutation	Average:21.118; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0112179197	C -> DEL	N	N	silent_mutation	Average:21.118; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0112179197	NA	5.43E-06	mr1128_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
vg0112179197	NA	4.39E-06	mr1184_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
vg0112179197	NA	1.04E-06	mr1204_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
vg0112179197	NA	8.25E-07	mr1289_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
vg0112179197	NA	6.41E-08	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
vg0112179197	NA	2.82E-06	mr1374_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
vg0112179197	1.01E-06	4.15E-07	mr1440_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
vg0112179197	1.06E-06	1.06E-06	mr1440_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
vg0112179197	NA	1.16E-08	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
vg0112179197	NA	4.73E-06	mr1556_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
vg0112179197	NA	8.64E-06	mr1556_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
vg0112179197	NA	9.06E-06	mr1646_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
vg0112179197	NA	2.38E-06	mr1665_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
vg0112179197	NA	1.21E-07	mr1683_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
vg0112179197	2.83E-06	1.00E-07	mr1687_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
vg0112179197	6.81E-06	6.81E-06	mr1687_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
vg0112179197	2.26E-06	2.26E-06	mr1811_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
vg0112179197	NA	2.70E-06	mr1896_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
vg0112179197	NA	6.99E-06	mr1984_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