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Detailed information for vg1019855843:

Variant ID: vg1019855843 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 19855843
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGAGATCGCTACTCCCGGGGGCAGCGGTGGCGGAAGCGTGAGAGCGGCACTAGATCGCCCGCTCTGATACCATGTTGGATAGTACAGGAAGAGGGGATAC[T/A]
GTGAATATTGGACACATTGTATTGAGCCTCAGGGGGGCGATATATATAGGAGTACATAGGGAAGAGATAAGGAAGAATTACAGATATAGAAGGAATCCAA

Reverse complement sequence

TTGGATTCCTTCTATATCTGTAATTCTTCCTTATCTCTTCCCTATGTACTCCTATATATATCGCCCCCCTGAGGCTCAATACAATGTGTCCAATATTCAC[A/T]
GTATCCCCTCTTCCTGTACTATCCAACATGGTATCAGAGCGGGCGATCTAGTGCCGCTCTCACGCTTCCGCCACCGCTGCCCCCGGGAGTAGCGATCTCC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	40.50%	1.30%	0.89%	57.36%	NA
All Indica	2759	19.90%	2.20%	1.27%	76.62%	NA
All Japonica	1512	70.00%	0.00%	0.13%	29.83%	NA
Aus	269	79.60%	0.00%	0.00%	20.45%	NA
Indica I	595	13.60%	4.00%	2.35%	80.00%	NA
Indica II	465	18.50%	0.20%	0.65%	80.65%	NA
Indica III	913	21.90%	3.00%	0.88%	74.26%	NA
Indica Intermediate	786	23.20%	1.10%	1.27%	74.43%	NA
Temperate Japonica	767	90.90%	0.00%	0.13%	9.00%	NA
Tropical Japonica	504	30.60%	0.00%	0.20%	69.25%	NA
Japonica Intermediate	241	86.30%	0.00%	0.00%	13.69%	NA
VI/Aromatic	96	49.00%	0.00%	4.17%	46.88%	NA
Intermediate	90	47.80%	0.00%	1.11%	51.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1019855843	T -> A	LOC_Os10g37090.1	5_prime_UTR_premature_start_codon_gain_variant ; LOW	silent_mutation	Average:22.677; most accessible tissue: Callus, score: 48.19	N	N	N	N
vg1019855843	T -> A	LOC_Os10g37090.1	5_prime_UTR_variant ; 422.0bp to feature; MODIFIER	silent_mutation	Average:22.677; most accessible tissue: Callus, score: 48.19	N	N	N	N
vg1019855843	T -> A	LOC_Os10g37079.1	upstream_gene_variant ; 3797.0bp to feature; MODIFIER	silent_mutation	Average:22.677; most accessible tissue: Callus, score: 48.19	N	N	N	N
vg1019855843	T -> A	LOC_Os10g37110.1	upstream_gene_variant ; 2769.0bp to feature; MODIFIER	silent_mutation	Average:22.677; most accessible tissue: Callus, score: 48.19	N	N	N	N
vg1019855843	T -> A	LOC_Os10g37100.1	downstream_gene_variant ; 780.0bp to feature; MODIFIER	silent_mutation	Average:22.677; most accessible tissue: Callus, score: 48.19	N	N	N	N
vg1019855843	T -> DEL	N	N	silent_mutation	Average:22.677; most accessible tissue: Callus, score: 48.19	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1019855843	NA	5.59E-06	mr1457_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
vg1019855843	7.66E-07	6.24E-09	mr1834_2	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