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Detailed information for vg0913926334:

Variant ID: vg0913926334 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 13926334
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTAAGTATACAACGGTGAAGTGAACATGGCTTAACTAGTTAACTAGTTATGTTTTTTTTAAACAACCCACGTACCTAGGTTCATGACCTAGACTAGAAA[T/C]
GGATTCTCGTATTTACGACTAATTATTTTTTCAGCGCTAGCCGACATACCCGTCAACATCGAGGTGCCCATGGTGACTTCGTCAATCTCAAAATATCTCA

Reverse complement sequence

TGAGATATTTTGAGATTGACGAAGTCACCATGGGCACCTCGATGTTGACGGGTATGTCGGCTAGCGCTGAAAAAATAATTAGTCGTAAATACGAGAATCC[A/G]
TTTCTAGTCTAGGTCATGAACCTAGGTACGTGGGTTGTTTAAAAAAAACATAACTAGTTAACTAGTTAAGCCATGTTCACTTCACCGTTGTATACTTAAT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.00%	7.00%	0.02%	0.00%	NA
All Indica	2759	97.30%	2.70%	0.00%	0.00%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	9.30%	90.30%	0.37%	0.00%	NA
Indica I	595	98.00%	2.00%	0.00%	0.00%	NA
Indica II	465	94.20%	5.80%	0.00%	0.00%	NA
Indica III	913	99.70%	0.30%	0.00%	0.00%	NA
Indica Intermediate	786	95.90%	4.10%	0.00%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	97.10%	2.90%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	3.30%	0.00%	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
vg0913926334	T -> C	LOC_Os09g23430.1	downstream_gene_variant ; 667.0bp to feature; MODIFIER	silent_mutation	Average:39.886; most accessible tissue: Zhenshan97 young leaf, score: 59.009	N	N	N	N
vg0913926334	T -> C	LOC_Os09g23430-LOC_Os09g23440	intergenic_region ; MODIFIER	silent_mutation	Average:39.886; most accessible tissue: Zhenshan97 young leaf, score: 59.009	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0913926334	3.39E-07	NA	mr1244_2	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
vg0913926334	NA	9.79E-11	mr1897_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