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Detailed information for vg0324085319:

Variant ID: vg0324085319 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 24085319
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CACCGTTGACGTCGAGCCGAGCCGTGCCGTCGTCGGAGCTCGTCGCCGGCCGCCGTACGTCGTCGTCCGTCGTAGTTTCTTGCACCGGTGAGTTCGTGTC[G/A]
TCGTCCTCTTCGCGTAGGTGTCCTCGGATAGCCCGGCCGAGCCCTCTATCGCCGGTGGTTGCGTCGTCCCGTGCCATGGCCGGCGATGATGTCATCGTGA

Reverse complement sequence

TCACGATGACATCATCGCCGGCCATGGCACGGGACGACGCAACCACCGGCGATAGAGGGCTCGGCCGGGCTATCCGAGGACACCTACGCGAAGAGGACGA[C/T]
GACACGAACTCACCGGTGCAAGAAACTACGACGGACGACGACGTACGGCGGCCGGCGACGAGCTCCGACGACGGCACGGCTCGGCTCGACGTCAACGGTG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	27.10%	13.00%	3.51%	56.41%	NA
All Indica	2759	3.40%	0.50%	2.72%	93.37%	NA
All Japonica	1512	56.70%	38.60%	3.84%	0.86%	NA
Aus	269	84.80%	0.00%	2.97%	12.27%	NA
Indica I	595	1.80%	0.30%	5.21%	92.61%	NA
Indica II	465	3.70%	0.00%	1.29%	95.05%	NA
Indica III	913	1.50%	0.70%	0.88%	96.93%	NA
Indica Intermediate	786	6.50%	0.90%	3.82%	88.80%	NA
Temperate Japonica	767	89.20%	6.40%	3.91%	0.52%	NA
Tropical Japonica	504	14.30%	81.70%	2.98%	0.99%	NA
Japonica Intermediate	241	42.30%	50.60%	5.39%	1.66%	NA
VI/Aromatic	96	79.20%	1.00%	13.54%	6.25%	NA
Intermediate	90	26.70%	17.80%	13.33%	42.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0324085319	G -> A	LOC_Os03g43180.1	synonymous_variant ; p.Asp26Asp; LOW	synonymous_codon	Average:13.708; most accessible tissue: Callus, score: 19.897	N	N	N	N
vg0324085319	G -> DEL	LOC_Os03g43180.1	N	frameshift_variant	Average:13.708; most accessible tissue: Callus, score: 19.897	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0324085319	NA	2.06E-06	mr1401	Jap_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
vg0324085319	NA	2.69E-07	mr1554	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
vg0324085319	NA	1.63E-28	mr1699	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
vg0324085319	9.81E-08	NA	mr1745	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
vg0324085319	NA	1.04E-12	mr1871	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
vg0324085319	NA	1.58E-22	mr1042_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
vg0324085319	NA	1.10E-06	mr1206_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
vg0324085319	NA	4.56E-06	mr1206_2	Jap_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
vg0324085319	NA	2.27E-09	mr1502_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
vg0324085319	NA	7.01E-09	mr1543_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
vg0324085319	NA	1.43E-28	mr1699_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
vg0324085319	NA	1.06E-14	mr1742_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
vg0324085319	NA	4.99E-07	mr1786_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
vg0324085319	NA	1.07E-23	mr1871_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