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Detailed information for vg0913080857:

Variant ID: vg0913080857 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 13080857
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGTTATAAATCGTCAGAAAGAAGATGAGGAAGTGTGCCAGCTGAAGAAAGCACTTGGAGAAGCCACTCGCATTGTAAATGTAAGTCTTCTAGGTAACTGC[C/T]
TTTGATGACTTTATTGTCTCGTTAGCAAAACTAATCCATGAACCACCATGCAGAGGATCCATCTTCGCAATGAGGCCAAGACCACAACCTTAGAAAAGCT

Reverse complement sequence

AGCTTTTCTAAGGTTGTGGTCTTGGCCTCATTGCGAAGATGGATCCTCTGCATGGTGGTTCATGGATTAGTTTTGCTAACGAGACAATAAAGTCATCAAA[G/A]
GCAGTTACCTAGAAGACTTACATTTACAATGCGAGTGGCTTCTCCAAGTGCTTTCTTCAGCTGGCACACTTCCTCATCTTCTTTCTGACGATTTATAACG

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	49.50%	31.00%	18.75%	0.76%	NA
All Indica	2759	51.00%	22.30%	26.21%	0.51%	NA
All Japonica	1512	48.70%	46.60%	3.31%	1.32%	NA
Aus	269	31.60%	40.10%	28.25%	0.00%	NA
Indica I	595	50.60%	9.40%	39.33%	0.67%	NA
Indica II	465	51.60%	19.80%	28.17%	0.43%	NA
Indica III	913	53.90%	29.20%	16.32%	0.55%	NA
Indica Intermediate	786	47.60%	25.40%	26.59%	0.38%	NA
Temperate Japonica	767	17.60%	77.30%	3.26%	1.83%	NA
Tropical Japonica	504	90.10%	6.20%	3.37%	0.40%	NA
Japonica Intermediate	241	61.40%	33.60%	3.32%	1.66%	NA
VI/Aromatic	96	74.00%	4.20%	21.88%	0.00%	NA
Intermediate	90	45.60%	34.40%	17.78%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0913080857	C -> DEL	N	N	silent_mutation	Average:8.76; most accessible tissue: Zhenshan97 young leaf, score: 22.751	N	N	N	N
vg0913080857	C -> T	LOC_Os09g21610.1	downstream_gene_variant ; 1258.0bp to feature; MODIFIER	silent_mutation	Average:8.76; most accessible tissue: Zhenshan97 young leaf, score: 22.751	N	N	N	N
vg0913080857	C -> T	LOC_Os09g21600.1	intron_variant ; MODIFIER	silent_mutation	Average:8.76; most accessible tissue: Zhenshan97 young leaf, score: 22.751	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0913080857	NA	8.94E-06	mr1182	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
vg0913080857	NA	1.33E-06	mr1057_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
vg0913080857	NA	7.46E-07	mr1347_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
vg0913080857	NA	3.08E-07	mr1379_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
vg0913080857	NA	1.73E-10	mr1551_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
vg0913080857	NA	1.34E-10	mr1552_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
vg0913080857	NA	5.64E-06	mr1606_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
vg0913080857	NA	1.30E-06	mr1905_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