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Detailed information for vg0414761828:

Variant ID: vg0414761828 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 14761828
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTGGCCGGTCTGACTGGCAGGTCCGAGTCCGACTGTGTTTCGTCGGGTCTCGAGGTTTCCTTGCTCGGGAAGGCATGTTTCGGGTTTCCTTTAGTTTCTA[C/T]
CCCGAGTTGGACATGGAGGAGGGCCTGTAGAGGGTAAGATCAACCCCTATATAAGGGATATGGCCGGTTCTATTGTAAAAAACCAATCGAATCGTTTTTC

Reverse complement sequence

GAAAAACGATTCGATTGGTTTTTTACAATAGAACCGGCCATATCCCTTATATAGGGGTTGATCTTACCCTCTACAGGCCCTCCTCCATGTCCAACTCGGG[G/A]
TAGAAACTAAAGGAAACCCGAAACATGCCTTCCCGAGCAAGGAAACCTCGAGACCCGACGAAACACAGTCGGACTCGGACCTGCCAGTCAGACCGGCCAC

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	84.40%	13.10%	1.78%	0.68%	NA
All Indica	2759	83.20%	13.70%	2.68%	0.47%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	3.00%	86.20%	3.72%	7.06%	NA
Indica I	595	89.10%	10.90%	0.00%	0.00%	NA
Indica II	465	72.50%	21.90%	3.87%	1.72%	NA
Indica III	913	82.90%	11.80%	5.04%	0.22%	NA
Indica Intermediate	786	85.40%	13.00%	1.27%	0.38%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	0.00%	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
vg0414761828	C -> DEL	N	N	silent_mutation	Average:61.251; most accessible tissue: Zhenshan97 panicle, score: 78.302	N	N	N	N
vg0414761828	C -> T	LOC_Os04g25454.1	upstream_gene_variant ; 2352.0bp to feature; MODIFIER	silent_mutation	Average:61.251; most accessible tissue: Zhenshan97 panicle, score: 78.302	N	N	N	N
vg0414761828	C -> T	LOC_Os04g25470.1	upstream_gene_variant ; 452.0bp to feature; MODIFIER	silent_mutation	Average:61.251; most accessible tissue: Zhenshan97 panicle, score: 78.302	N	N	N	N
vg0414761828	C -> T	LOC_Os04g25454-LOC_Os04g25470	intergenic_region ; MODIFIER	silent_mutation	Average:61.251; most accessible tissue: Zhenshan97 panicle, score: 78.302	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0414761828	NA	1.40E-06	mr1045	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
vg0414761828	NA	8.33E-08	mr1193	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
vg0414761828	NA	2.08E-09	mr1815	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
vg0414761828	NA	9.25E-08	mr1951	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
vg0414761828	NA	7.73E-07	mr1968	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
vg0414761828	NA	4.00E-07	mr1498_2	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