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Detailed information for vg0401225828:

Variant ID: vg0401225828 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 1225828
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAGTGTTGGTGTTTGTCAGGGTTATGGATACCACATACCTAATAGTAGTTGATTAAATCTCGGCAAGACCCACTACATACCATGTACTATACGGAAATAA[C/T]
CTGTGGATATAGGAGGAGTTCCGGATAAGGAAAGATAACCAGAATTCTATATGAAAACGACAAGGACTACTCGGATTGTATCCATATTGGTTTCCCTAGT

Reverse complement sequence

ACTAGGGAAACCAATATGGATACAATCCGAGTAGTCCTTGTCGTTTTCATATAGAATTCTGGTTATCTTTCCTTATCCGGAACTCCTCCTATATCCACAG[G/A]
TTATTTCCGTATAGTACATGGTATGTAGTGGGTCTTGCCGAGATTTAATCAACTACTATTAGGTATGTGGTATCCATAACCCTGACAAACACCAACACTC

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	87.90%	4.80%	3.41%	3.83%	NA
All Indica	2759	91.70%	1.30%	1.05%	5.94%	NA
All Japonica	1512	78.00%	12.50%	8.53%	0.99%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	98.70%	1.00%	0.34%	0.00%	NA
Indica II	465	80.20%	1.90%	1.51%	16.34%	NA
Indica III	913	89.90%	2.00%	1.10%	7.01%	NA
Indica Intermediate	786	95.20%	0.50%	1.27%	3.05%	NA
Temperate Japonica	767	62.20%	21.80%	14.21%	1.83%	NA
Tropical Japonica	504	96.00%	1.60%	2.38%	0.00%	NA
Japonica Intermediate	241	90.50%	5.80%	3.32%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	92.20%	2.20%	3.33%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0401225828	C -> DEL	N	N	silent_mutation	Average:52.912; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N
vg0401225828	C -> T	LOC_Os04g03000.1	upstream_gene_variant ; 1477.0bp to feature; MODIFIER	silent_mutation	Average:52.912; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N
vg0401225828	C -> T	LOC_Os04g03010.1	upstream_gene_variant ; 665.0bp to feature; MODIFIER	silent_mutation	Average:52.912; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N
vg0401225828	C -> T	LOC_Os04g02990.1	downstream_gene_variant ; 4399.0bp to feature; MODIFIER	silent_mutation	Average:52.912; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N
vg0401225828	C -> T	LOC_Os04g03020.1	downstream_gene_variant ; 4074.0bp to feature; MODIFIER	silent_mutation	Average:52.912; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N
vg0401225828	C -> T	LOC_Os04g03000-LOC_Os04g03010	intergenic_region ; MODIFIER	silent_mutation	Average:52.912; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0401225828	NA	1.90E-07	mr1723	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
vg0401225828	1.63E-06	NA	mr1670_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