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Detailed information for vg0420557418:

Variant ID: vg0420557418 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 20557418
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGGAAACTATGTCTTGCATGAGACATGGTTTTTACACAAACATCCAAGACATTATGTGAGATAAGTAGCATTAAATTTAAGTATGAAATAGTGGTGTTTG[C/T]
ATTGGAAGAGTAGTGTCTAGTACTAATTTCTTAATGATGTGGAGTTTATGAAAACTACGTCTAGTATTTTGGGTTGAGAATAGCCTTAATATATATCATA

Reverse complement sequence

TATGATATATATTAAGGCTATTCTCAACCCAAAATACTAGACGTAGTTTTCATAAACTCCACATCATTAAGAAATTAGTACTAGACACTACTCTTCCAAT[G/A]
CAAACACCACTATTTCATACTTAAATTTAATGCTACTTATCTCACATAATGTCTTGGATGTTTGTGTAAAAACCATGTCTCATGCAAGACATAGTTTCCT

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	94.30%	4.70%	0.99%	0.00%	NA
All Indica	2759	99.70%	0.20%	0.07%	0.00%	NA
All Japonica	1512	86.00%	11.30%	2.71%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.60%	0.30%	0.11%	0.00%	NA
Indica Intermediate	786	99.60%	0.30%	0.13%	0.00%	NA
Temperate Japonica	767	97.30%	1.00%	1.69%	0.00%	NA
Tropical Japonica	504	68.30%	28.40%	3.37%	0.00%	NA
Japonica Intermediate	241	87.10%	8.30%	4.56%	0.00%	NA
VI/Aromatic	96	61.50%	36.50%	2.08%	0.00%	NA
Intermediate	90	85.60%	12.20%	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
vg0420557418	C -> T	LOC_Os04g33950.1	upstream_gene_variant ; 2114.0bp to feature; MODIFIER	silent_mutation	Average:44.475; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N
vg0420557418	C -> T	LOC_Os04g33970.1	upstream_gene_variant ; 2548.0bp to feature; MODIFIER	silent_mutation	Average:44.475; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N
vg0420557418	C -> T	LOC_Os04g33960.1	intron_variant ; MODIFIER	silent_mutation	Average:44.475; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0420557418	NA	1.18E-06	mr1578	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
vg0420557418	NA	2.17E-06	mr1606	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
vg0420557418	1.16E-06	8.58E-08	mr1819	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
vg0420557418	NA	5.81E-06	mr1866	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