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Detailed information for vg0119705377:

Variant ID: vg0119705377 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 19705377
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCTCGGCTATCTAATCCGCTAGGTCTATACCCATACGAGAAGTGCGGTTGTACGGGGGTCATTTCATGCTTAACTTCATGGCTCGGTCCTTAATTGACCG[T/G]
GGACGGTACTAGCCATTTCCAGATACCACCCAAATCCTCCGTCCGCCCCAGTCGAAAACAGTTGTTTAGTTTTATTTCTCCTTTCACAAATCATGTCATC

Reverse complement sequence

GATGACATGATTTGTGAAAGGAGAAATAAAACTAAACAACTGTTTTCGACTGGGGCGGACGGAGGATTTGGGTGGTATCTGGAAATGGCTAGTACCGTCC[A/C]
CGGTCAATTAAGGACCGAGCCATGAAGTTAAGCATGAAATGACCCCCGTACAACCGCACTTCTCGTATGGGTATAGACCTAGCGGATTAGATAGCCGAGC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	67.50%	0.50%	19.00%	12.99%	NA
All Indica	2759	46.90%	0.80%	30.88%	21.42%	NA
All Japonica	1512	99.20%	0.00%	0.46%	0.33%	NA
Aus	269	83.60%	0.00%	11.52%	4.83%	NA
Indica I	595	44.50%	0.00%	17.65%	37.82%	NA
Indica II	465	74.00%	0.00%	16.34%	9.68%	NA
Indica III	913	29.90%	1.90%	49.84%	18.40%	NA
Indica Intermediate	786	52.40%	0.60%	27.48%	19.47%	NA
Temperate Japonica	767	99.70%	0.00%	0.00%	0.26%	NA
Tropical Japonica	504	99.40%	0.00%	0.40%	0.20%	NA
Japonica Intermediate	241	97.10%	0.00%	2.07%	0.83%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	86.70%	0.00%	7.78%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0119705377	T -> G	LOC_Os01g35600.1	upstream_gene_variant ; 316.0bp to feature; MODIFIER	silent_mutation	Average:39.983; most accessible tissue: Minghui63 young leaf, score: 77.654	N	N	N	N
vg0119705377	T -> G	LOC_Os01g35610.1	upstream_gene_variant ; 4691.0bp to feature; MODIFIER	silent_mutation	Average:39.983; most accessible tissue: Minghui63 young leaf, score: 77.654	N	N	N	N
vg0119705377	T -> G	LOC_Os01g35600-LOC_Os01g35610	intergenic_region ; MODIFIER	silent_mutation	Average:39.983; most accessible tissue: Minghui63 young leaf, score: 77.654	N	N	N	N
vg0119705377	T -> DEL	N	N	silent_mutation	Average:39.983; most accessible tissue: Minghui63 young leaf, score: 77.654	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0119705377	NA	1.90E-09	mr1739_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
vg0119705377	3.81E-06	3.81E-06	mr1978_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