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Detailed information for vg0424368741:

Variant ID: vg0424368741 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 24368741
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAAAAACGCCGAAGGAAATTTGGGACAAGTTGGCAAGCCTGTATATGTCCAAGTCGCTGACGAGTAAGTTGTATCTCAAACAACAGTCGTATGGTTTGCA[A/G]
ATGCAAGAGGAGTCAGATCTTAGGAAGCACGTGGACATCTTCAATCAGTTGGTTGTGGATCTAAGAAAGTTAGATGTGAAACTGGATGATGAAGACAAGG

Reverse complement sequence

CCTTGTCTTCATCATCCAGTTTCACATCTAACTTTCTTAGATCCACAACCAACTGATTGAAGATGTCCACGTGCTTCCTAAGATCTGACTCCTCTTGCAT[T/C]
TGCAAACCATACGACTGTTGTTTGAGATACAACTTACTCGTCAGCGACTTGGACATATACAGGCTTGCCAACTTGTCCCAAATTTCCTTCGGCGTTTTTT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	75.50%	23.80%	0.63%	0.00%	NA
All Indica	2759	62.90%	36.60%	0.54%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.07%	0.00%	NA
Aus	269	57.20%	37.90%	4.83%	0.00%	NA
Indica I	595	73.10%	26.70%	0.17%	0.00%	NA
Indica II	465	95.50%	4.30%	0.22%	0.00%	NA
Indica III	913	42.10%	57.20%	0.77%	0.00%	NA
Indica Intermediate	786	60.10%	39.20%	0.76%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	83.30%	15.60%	1.11%	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
vg0424368741	A -> G	LOC_Os04g41090.1	synonymous_variant ; p.Gln65Gln; LOW	synonymous_codon	Average:38.054; most accessible tissue: Zhenshan97 young leaf, score: 51.334	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0424368741	1.22E-06	NA	mr1375	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
vg0424368741	NA	5.98E-06	mr1798	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
vg0424368741	NA	2.02E-07	mr1798_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