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Detailed information for vg1004450805:

Variant ID: vg1004450805 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 4450805
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGACGAAGCCTACTCCTCGGAAAAGTCACCATCCGACGCATACTCAAACTCTGGGGTTTTGGGGAAAATAGAGCAAGACTGAGTACAACCACCGTACTCA[G/A]
CAAGTCATACCGGAACAGGGGGTATGATGCAGGATATAACCAAAGGATAGCTAAAGCGGTTCATTTGCATAAATTGAGCATTTATAAACAGTAGTTGAAA

Reverse complement sequence

TTTCAACTACTGTTTATAAATGCTCAATTTATGCAAATGAACCGCTTTAGCTATCCTTTGGTTATATCCTGCATCATACCCCCTGTTCCGGTATGACTTG[C/T]
TGAGTACGGTGGTTGTACTCAGTCTTGCTCTATTTTCCCCAAAACCCCAGAGTTTGAGTATGCGTCGGATGGTGACTTTTCCGAGGAGTAGGCTTCGTCC

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	71.60%	9.60%	0.85%	17.92%	NA
All Indica	2759	83.00%	0.70%	1.09%	15.22%	NA
All Japonica	1512	62.00%	26.10%	0.20%	11.64%	NA
Aus	269	16.00%	0.00%	1.49%	82.53%	NA
Indica I	595	65.70%	0.00%	1.68%	32.61%	NA
Indica II	465	82.60%	0.20%	0.86%	16.34%	NA
Indica III	913	91.50%	0.80%	1.31%	6.46%	NA
Indica Intermediate	786	86.50%	1.40%	0.51%	11.58%	NA
Temperate Japonica	767	89.20%	5.50%	0.00%	5.35%	NA
Tropical Japonica	504	26.80%	59.50%	0.40%	13.29%	NA
Japonica Intermediate	241	49.40%	22.00%	0.41%	28.22%	NA
VI/Aromatic	96	50.00%	26.00%	3.12%	20.83%	NA
Intermediate	90	74.40%	15.60%	0.00%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1004450805	G -> A	LOC_Os10g08230.1	downstream_gene_variant ; 3509.0bp to feature; MODIFIER	silent_mutation	Average:18.454; most accessible tissue: Callus, score: 30.618	N	N	N	N
vg1004450805	G -> A	LOC_Os10g08240.1	intron_variant ; MODIFIER	silent_mutation	Average:18.454; most accessible tissue: Callus, score: 30.618	N	N	N	N
vg1004450805	G -> DEL	N	N	silent_mutation	Average:18.454; most accessible tissue: Callus, score: 30.618	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1004450805	4.71E-06	NA	mr1021	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
vg1004450805	NA	5.73E-07	mr1248	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
vg1004450805	NA	6.99E-09	mr1248	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
vg1004450805	2.10E-06	NA	mr1471	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
vg1004450805	NA	1.25E-08	mr1471	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
vg1004450805	1.08E-07	NA	mr1477	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
vg1004450805	NA	1.15E-12	mr1553	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
vg1004450805	NA	3.77E-10	mr1642	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
vg1004450805	NA	1.10E-06	mr1642	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
vg1004450805	NA	4.41E-06	mr1782	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
vg1004450805	NA	9.53E-07	mr1797	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
vg1004450805	NA	9.53E-07	mr1801	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
vg1004450805	NA	8.54E-07	mr1553_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
vg1004450805	NA	1.16E-06	mr1632_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
vg1004450805	NA	4.21E-07	mr1696_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
vg1004450805	NA	6.21E-08	mr1817_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