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Detailed information for vg0514228183:

Variant ID: vg0514228183 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 14228183
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTGGTAATACCAACCGGGACTAAAGTTACGATCTTTAGTCCCGGTTGGTAATACCAACCATTACCAACCGGGACTAAAGATCCTAGAGGGGCCTGACATG[C/T]
CCTGACAGCATTCGAACCGGGACTAAAGATGATCCTTAGTCCCGGTTGGTGTGTTACCAACCAGGACTAAAGATCAAATATGCCCGTTACCCTTTTGAAC

Reverse complement sequence

GTTCAAAAGGGTAACGGGCATATTTGATCTTTAGTCCTGGTTGGTAACACACCAACCGGGACTAAGGATCATCTTTAGTCCCGGTTCGAATGCTGTCAGG[G/A]
CATGTCAGGCCCCTCTAGGATCTTTAGTCCCGGTTGGTAATGGTTGGTATTACCAACCGGGACTAAAGATCGTAACTTTAGTCCCGGTTGGTATTACCAA

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	80.30%	0.30%	0.21%	19.19%	NA
All Indica	2759	67.90%	0.40%	0.36%	31.28%	NA
All Japonica	1512	98.50%	0.00%	0.00%	1.52%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	45.20%	0.70%	0.17%	53.95%	NA
Indica II	465	72.00%	0.00%	0.43%	27.53%	NA
Indica III	913	79.50%	0.50%	0.11%	19.82%	NA
Indica Intermediate	786	69.20%	0.40%	0.76%	29.64%	NA
Temperate Japonica	767	97.80%	0.00%	0.00%	2.22%	NA
Tropical Japonica	504	99.20%	0.00%	0.00%	0.79%	NA
Japonica Intermediate	241	99.20%	0.00%	0.00%	0.83%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	76.70%	0.00%	0.00%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0514228183	C -> T	LOC_Os05g24620.1	upstream_gene_variant ; 1121.0bp to feature; MODIFIER	silent_mutation	Average:45.471; most accessible tissue: Zhenshan97 root, score: 86.252	N	N	N	N
vg0514228183	C -> T	LOC_Os05g24630.1	upstream_gene_variant ; 3094.0bp to feature; MODIFIER	silent_mutation	Average:45.471; most accessible tissue: Zhenshan97 root, score: 86.252	N	N	N	N
vg0514228183	C -> T	LOC_Os05g24620-LOC_Os05g24630	intergenic_region ; MODIFIER	silent_mutation	Average:45.471; most accessible tissue: Zhenshan97 root, score: 86.252	N	N	N	N
vg0514228183	C -> DEL	N	N	silent_mutation	Average:45.471; most accessible tissue: Zhenshan97 root, score: 86.252	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0514228183	NA	7.13E-07	mr1074_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
vg0514228183	NA	5.54E-07	mr1170_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
vg0514228183	NA	9.08E-07	mr1240_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
vg0514228183	NA	1.79E-06	mr1266_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
vg0514228183	4.73E-06	4.70E-06	mr1413_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
vg0514228183	NA	7.92E-07	mr1551_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