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Detailed information for vg0127881125:

Variant ID: vg0127881125 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 27881125
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

TAGTTTCTTCTCTGAAAAAATAAATTACAACAAAATAAATAATATTTTTATTTTTTTAATAGGATAAATGATTAGAATTACTATTGGGAGCTCCAAGCGC[G/C]
AAACGTGTATCAGCCAGGCCCACCTCACCCCACGTTCCATCATCTCGCTCCCACCGTTATCGGAGTAAACGATTTACTTAGATAAAAACAGCTTCTCTGG

Reverse complement sequence

CCAGAGAAGCTGTTTTTATCTAAGTAAATCGTTTACTCCGATAACGGTGGGAGCGAGATGATGGAACGTGGGGTGAGGTGGGCCTGGCTGATACACGTTT[C/G]
GCGCTTGGAGCTCCCAATAGTAATTCTAATCATTTATCCTATTAAAAAAATAAAAATATTATTTATTTTGTTGTAATTTATTTTTTCAGAGAAGAAACTA

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	29.20%	21.80%	2.71%	46.30%	NA
All Indica	2759	1.30%	16.20%	4.60%	77.85%	NA
All Japonica	1512	86.30%	13.30%	0.00%	0.40%	NA
Aus	269	0.40%	96.70%	0.37%	2.60%	NA
Indica I	595	0.70%	17.10%	3.87%	78.32%	NA
Indica II	465	2.80%	3.20%	6.02%	87.96%	NA
Indica III	913	0.40%	25.60%	3.50%	70.43%	NA
Indica Intermediate	786	1.90%	12.30%	5.60%	80.15%	NA
Temperate Japonica	767	99.70%	0.00%	0.00%	0.26%	NA
Tropical Japonica	504	62.10%	37.50%	0.00%	0.40%	NA
Japonica Intermediate	241	94.20%	5.00%	0.00%	0.83%	NA
VI/Aromatic	96	2.10%	94.80%	0.00%	3.12%	NA
Intermediate	90	41.10%	32.20%	0.00%	26.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0127881125	G -> DEL	N	N	silent_mutation	Average:37.252; most accessible tissue: Zhenshan97 flag leaf, score: 60.074	N	N	N	N
vg0127881125	G -> C	LOC_Os01g48640.1	upstream_gene_variant ; 1895.0bp to feature; MODIFIER	silent_mutation	Average:37.252; most accessible tissue: Zhenshan97 flag leaf, score: 60.074	N	N	N	N
vg0127881125	G -> C	LOC_Os01g48620.1	downstream_gene_variant ; 2665.0bp to feature; MODIFIER	silent_mutation	Average:37.252; most accessible tissue: Zhenshan97 flag leaf, score: 60.074	N	N	N	N
vg0127881125	G -> C	LOC_Os01g48620-LOC_Os01g48640	intergenic_region ; MODIFIER	silent_mutation	Average:37.252; most accessible tissue: Zhenshan97 flag leaf, score: 60.074	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0127881125	NA	8.63E-58	mr1019	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
vg0127881125	5.21E-07	NA	mr1083_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
vg0127881125	5.20E-06	NA	mr1088_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
vg0127881125	1.23E-08	NA	mr1103_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
vg0127881125	1.91E-08	NA	mr1104_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
vg0127881125	2.76E-06	NA	mr1145_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
vg0127881125	NA	2.17E-13	mr1217_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
vg0127881125	NA	1.33E-06	mr1227_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
vg0127881125	5.07E-06	NA	mr1246_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
vg0127881125	NA	8.92E-53	mr1261_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
vg0127881125	NA	3.35E-10	mr1282_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
vg0127881125	NA	1.92E-20	mr1298_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
vg0127881125	5.94E-06	NA	mr1517_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
vg0127881125	NA	8.64E-28	mr1584_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
vg0127881125	NA	7.33E-08	mr1607_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
vg0127881125	NA	8.46E-18	mr1682_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
vg0127881125	NA	3.24E-18	mr1730_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
vg0127881125	NA	8.71E-20	mr1731_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