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Detailed information for vg0910315478:

Variant ID: vg0910315478 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 10315478
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AACGTGAACGAACGCGAACGAACATGAACAAAACGTGAACGAACGGGAACGAACGCGAACGAACGTGATTGAAACGTGAACGAACGTGAACGAATGCGAA[C/T]
GAACGCGAACGAACGTGAACGAACGTGAACGAACGCGAACGAACGAGAACGAACGCGAACGAACGTGATTGAAACGTGAACGAACGCGAACGAACGTAAA

Reverse complement sequence

TTTACGTTCGTTCGCGTTCGTTCACGTTTCAATCACGTTCGTTCGCGTTCGTTCTCGTTCGTTCGCGTTCGTTCACGTTCGTTCACGTTCGTTCGCGTTC[G/A]
TTCGCATTCGTTCACGTTCGTTCACGTTTCAATCACGTTCGTTCGCGTTCGTTCCCGTTCGTTCACGTTTTGTTCATGTTCGTTCGCGTTCGTTCACGTT

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	96.30%	2.40%	0.32%	0.99%	NA
All Indica	2759	95.70%	2.70%	0.47%	1.20%	NA
All Japonica	1512	98.90%	0.10%	0.00%	0.93%	NA
Aus	269	86.60%	12.60%	0.74%	0.00%	NA
Indica I	595	99.30%	0.70%	0.00%	0.00%	NA
Indica II	465	89.50%	7.10%	1.51%	1.94%	NA
Indica III	913	97.60%	1.10%	0.00%	1.31%	NA
Indica Intermediate	786	94.30%	3.40%	0.76%	1.53%	NA
Temperate Japonica	767	98.00%	0.10%	0.00%	1.83%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	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
vg0910315478	C -> DEL	N	N	silent_mutation	Average:24.705; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N
vg0910315478	C -> T	LOC_Os09g16890.1	upstream_gene_variant ; 844.0bp to feature; MODIFIER	silent_mutation	Average:24.705; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N
vg0910315478	C -> T	LOC_Os09g16880.1	downstream_gene_variant ; 1396.0bp to feature; MODIFIER	silent_mutation	Average:24.705; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N
vg0910315478	C -> T	LOC_Os09g16880-LOC_Os09g16890	intergenic_region ; MODIFIER	silent_mutation	Average:24.705; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0910315478	NA	5.63E-06	mr1539_2	Ind_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
vg0910315478	NA	3.35E-06	mr1540_2	Ind_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
vg0910315478	NA	5.72E-06	mr1717_2	Ind_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
vg0910315478	NA	1.71E-06	mr1732_2	Ind_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
vg0910315478	NA	3.41E-07	mr1748_2	Ind_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
vg0910315478	NA	6.41E-07	mr1895_2	Ind_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