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Detailed information for vg0912682054:

Variant ID: vg0912682054 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 12682054
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGCAGGTCTCCGGAACCTCTGCCTTCGACGTCCTGCACCGGGAGAAGGCGGCAATAAGGTTTTTGGGAAGCGCTTTGCGCGACTGCTCCCTGTTCGTCTG[C/T]
GACGGCTCGTCTTCCTCTTTACTCGCGTGCTTCGTGCCTTTGTAGATGCCTGCGAAAAGTTTCGACCGAGCAGCCGGTCTTTCCGCCACCTCGGTACGTG

Reverse complement sequence

CACGTACCGAGGTGGCGGAAAGACCGGCTGCTCGGTCGAAACTTTTCGCAGGCATCTACAAAGGCACGAAGCACGCGAGTAAAGAGGAAGACGAGCCGTC[G/A]
CAGACGAACAGGGAGCAGTCGCGCAAAGCGCTTCCCAAAAACCTTATTGCCGCCTTCTCCCGGTGCAGGACGTCGAAGGCAGAGGTTCCGGAGACCTGCT

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	98.30%	1.20%	0.53%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.04%	0.00%	NA
All Japonica	1512	94.90%	3.60%	1.52%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	93.50%	4.80%	1.69%	0.00%	NA
Tropical Japonica	504	99.20%	0.20%	0.60%	0.00%	NA
Japonica Intermediate	241	90.50%	6.60%	2.90%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	0.00%	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
vg0912682054	C -> T	LOC_Os09g21030.1	downstream_gene_variant ; 2627.0bp to feature; MODIFIER	silent_mutation	Average:57.734; most accessible tissue: Zhenshan97 panicle, score: 76.605	N	N	N	N
vg0912682054	C -> T	LOC_Os09g21040.1	downstream_gene_variant ; 3692.0bp to feature; MODIFIER	silent_mutation	Average:57.734; most accessible tissue: Zhenshan97 panicle, score: 76.605	N	N	N	N
vg0912682054	C -> T	LOC_Os09g21020.1	intron_variant ; MODIFIER	silent_mutation	Average:57.734; most accessible tissue: Zhenshan97 panicle, score: 76.605	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0912682054	5.84E-07	4.70E-07	mr1038_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
vg0912682054	6.05E-08	6.05E-08	mr1389_2	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