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Detailed information for vg0419331192:

Variant ID: vg0419331192 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 19331192
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTAGGTGATTGATACAAGGAGATATTTCACCGAGAAATCAACAAAGGTTGCTGCATCTGCATGCAAGCATCCATCCATCTAGCACAGACTCATCGTACGG[C/T]
TAATATTTGACACCGTTGACTTTTTAACACATGTTTGACCATTCATCTTATTTAAAAACTTTTGTGAAATATATAAAACTATATGTATACATATAAGTAT

Reverse complement sequence

ATACTTATATGTATACATATAGTTTTATATATTTCACAAAAGTTTTTAAATAAGATGAATGGTCAAACATGTGTTAAAAAGTCAACGGTGTCAAATATTA[G/A]
CCGTACGATGAGTCTGTGCTAGATGGATGGATGCTTGCATGCAGATGCAGCAACCTTTGTTGATTTCTCGGTGAAATATCTCCTTGTATCAATCACCTAA

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	46.30%	0.40%	0.11%	53.17%	NA
All Indica	2759	10.80%	0.60%	0.14%	88.40%	NA
All Japonica	1512	99.70%	0.00%	0.00%	0.26%	NA
Aus	269	79.60%	0.40%	0.37%	19.70%	NA
Indica I	595	15.30%	1.00%	0.00%	83.70%	NA
Indica II	465	12.90%	0.20%	0.00%	86.88%	NA
Indica III	913	3.90%	0.50%	0.11%	95.40%	NA
Indica Intermediate	786	14.20%	0.60%	0.38%	84.73%	NA
Temperate Japonica	767	99.70%	0.00%	0.00%	0.26%	NA
Tropical Japonica	504	99.60%	0.00%	0.00%	0.40%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	81.10%	0.00%	0.00%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0419331192	C -> DEL	N	N	silent_mutation	Average:40.706; most accessible tissue: Callus, score: 80.403	N	N	N	N
vg0419331192	C -> T	LOC_Os04g32250.1	downstream_gene_variant ; 4041.0bp to feature; MODIFIER	silent_mutation	Average:40.706; most accessible tissue: Callus, score: 80.403	N	N	N	N
vg0419331192	C -> T	LOC_Os04g32270.1	downstream_gene_variant ; 3318.0bp to feature; MODIFIER	silent_mutation	Average:40.706; most accessible tissue: Callus, score: 80.403	N	N	N	N
vg0419331192	C -> T	LOC_Os04g32270.2	downstream_gene_variant ; 4826.0bp to feature; MODIFIER	silent_mutation	Average:40.706; most accessible tissue: Callus, score: 80.403	N	N	N	N
vg0419331192	C -> T	LOC_Os04g32260.1	intron_variant ; MODIFIER	silent_mutation	Average:40.706; most accessible tissue: Callus, score: 80.403	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0419331192	NA	8.33E-15	mr1165	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
vg0419331192	NA	6.31E-06	mr1189	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
vg0419331192	7.71E-06	NA	mr1382	Ind_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
vg0419331192	NA	5.32E-06	mr1851	Ind_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