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Detailed information for vg0121578906:

Variant ID: vg0121578906 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 21578906
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.04, others allele: 0.00, population size: 28. )

Flanking Sequence (100 bp) in Reference Genome:

ACCGTGTGTACACTGTACTGGTGCACACGCATGTGCTGTATATGCAGGGCTTGTATTCCGATCCATGTAGGTTGTCACACCCTGAAGTTTTTCCCCCAAG[C/T]
CTAAATTGAATTTATAAATCACCTTGAGAAAATACCAGACTCAAAGCAAGAGAACCCTAATAAAGTAATGCAAATAATAATCGGAATTGGCATGTGGGAT

Reverse complement sequence

ATCCCACATGCCAATTCCGATTATTATTTGCATTACTTTATTAGGGTTCTCTTGCTTTGAGTCTGGTATTTTCTCAAGGTGATTTATAAATTCAATTTAG[G/A]
CTTGGGGGAAAAACTTCAGGGTGTGACAACCTACATGGATCGGAATACAAGCCCTGCATATACAGCACATGCGTGTGCACCAGTACAGTGTACACACGGT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	25.70%	8.80%	16.46%	49.05%	NA
All Indica	2759	3.00%	0.50%	23.92%	72.60%	NA
All Japonica	1512	67.40%	25.60%	3.44%	3.57%	NA
Aus	269	4.80%	0.00%	20.07%	75.09%	NA
Indica I	595	0.80%	0.00%	11.43%	87.73%	NA
Indica II	465	3.70%	0.60%	18.71%	76.99%	NA
Indica III	913	2.00%	0.30%	35.05%	62.65%	NA
Indica Intermediate	786	5.50%	0.90%	23.54%	70.10%	NA
Temperate Japonica	767	92.30%	2.30%	1.83%	3.52%	NA
Tropical Japonica	504	26.40%	65.90%	5.75%	1.98%	NA
Japonica Intermediate	241	73.90%	15.40%	3.73%	7.05%	NA
VI/Aromatic	96	68.80%	0.00%	3.12%	28.12%	NA
Intermediate	90	37.80%	16.70%	10.00%	35.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0121578906	C -> T	LOC_Os01g38400-LOC_Os01g38410	intergenic_region ; MODIFIER	silent_mutation	Average:14.531; most accessible tissue: Callus, score: 54.079	N	N	N	N
vg0121578906	C -> DEL	N	N	silent_mutation	Average:14.531; most accessible tissue: Callus, score: 54.079	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0121578906	NA	4.42E-09	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
vg0121578906	NA	1.19E-10	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
vg0121578906	NA	3.85E-06	mr1425	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
vg0121578906	NA	9.89E-06	mr1425	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
vg0121578906	NA	2.44E-09	mr1539	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
vg0121578906	NA	1.89E-09	mr1580	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
vg0121578906	5.00E-08	1.04E-42	mr1699	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
vg0121578906	8.75E-06	1.95E-22	mr1699	Jap_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
vg0121578906	NA	4.04E-21	mr1715	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
vg0121578906	NA	5.04E-07	mr1733	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
vg0121578906	NA	2.57E-11	mr1769	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
vg0121578906	NA	4.37E-15	mr1769	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
vg0121578906	NA	1.73E-06	mr1993	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
vg0121578906	NA	5.54E-07	mr1668_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
vg0121578906	NA	1.77E-07	mr1676_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
vg0121578906	NA	1.29E-36	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
vg0121578906	NA	1.06E-18	mr1699_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
vg0121578906	NA	1.08E-11	mr1769_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