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Detailed information for vg0414030990:

Variant ID: vg0414030990 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 14030990
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGCTGTCTCGAAGGCTGGAGCGTTGTGGCAGCAAGGTTGCCGTTATGGGAGGACGACAAGGCCATGATGAAGTGGCTAGGTGGCCCATTGCATAGATGAC[A/T]
CGGGCAGCCTGGCCAAGGCGGCGATGATGGTAGCGCCATTTGGTGGGCATCAGCCCTCTTGCAGTGGCATCTCGCCACCACAAGATGGTCACGTGGGGGA

Reverse complement sequence

TCCCCCACGTGACCATCTTGTGGTGGCGAGATGCCACTGCAAGAGGGCTGATGCCCACCAAATGGCGCTACCATCATCGCCGCCTTGGCCAGGCTGCCCG[T/A]
GTCATCTATGCAATGGGCCACCTAGCCACTTCATCATGGCCTTGTCGTCCTCCCATAACGGCAACCTTGCTGCCACAACGCTCCAGCCTTCGAGACAGCC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	81.60%	4.30%	11.60%	2.52%	NA
All Indica	2759	70.00%	7.10%	18.70%	4.13%	NA
All Japonica	1512	99.70%	0.00%	0.26%	0.00%	NA
Aus	269	88.10%	1.50%	8.55%	1.86%	NA
Indica I	595	73.80%	2.90%	19.66%	3.70%	NA
Indica II	465	75.90%	2.60%	19.57%	1.94%	NA
Indica III	913	59.60%	13.30%	20.59%	6.57%	NA
Indica Intermediate	786	75.80%	6.00%	15.27%	2.93%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.00%	0.60%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	92.20%	2.20%	5.56%	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
vg0414030990	A -> DEL	N	N	silent_mutation	Average:22.68; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N
vg0414030990	A -> T	LOC_Os04g24460.1	downstream_gene_variant ; 1803.0bp to feature; MODIFIER	silent_mutation	Average:22.68; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N
vg0414030990	A -> T	LOC_Os04g24460-LOC_Os04g24469	intergenic_region ; MODIFIER	silent_mutation	Average:22.68; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0414030990	4.07E-06	NA	mr1404	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
vg0414030990	1.25E-06	4.40E-06	mr1404	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