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Detailed information for vg0910817608:

Variant ID: vg0910817608 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 10817608
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCTCTCAGAAGTACTCATAGGGGTATATGCATGTGTGTGGTGGAACTTGACCACTCGGGTACAAGTCTTAGACTTGACAAATTCTTTCAATGATAGGCGA[C/T]
GTAACAGTCGACAACGAGGTGCGTGGCAACTTCGTAAATGTCAAAATATGTCTACCTAATCTCTCAGAAGTACTCATAGGGGTATATGCATGTATGCATT

Reverse complement sequence

AATGCATACATGCATATACCCCTATGAGTACTTCTGAGAGATTAGGTAGACATATTTTGACATTTACGAAGTTGCCACGCACCTCGTTGTCGACTGTTAC[G/A]
TCGCCTATCATTGAAAGAATTTGTCAAGTCTAAGACTTGTACCCGAGTGGTCAAGTTCCACCACACACATGCATATACCCCTATGAGTACTTCTGAGAGA

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	90.10%	1.90%	1.14%	6.86%	NA
All Indica	2759	88.30%	0.20%	0.65%	10.91%	NA
All Japonica	1512	92.80%	5.20%	2.05%	0.00%	NA
Aus	269	91.40%	0.00%	1.49%	7.06%	NA
Indica I	595	90.80%	0.00%	0.50%	8.74%	NA
Indica II	465	97.40%	0.40%	0.22%	1.94%	NA
Indica III	913	80.30%	0.00%	0.99%	18.73%	NA
Indica Intermediate	786	90.20%	0.40%	0.64%	8.78%	NA
Temperate Japonica	767	97.30%	0.40%	2.35%	0.00%	NA
Tropical Japonica	504	84.90%	12.70%	2.38%	0.00%	NA
Japonica Intermediate	241	95.00%	4.60%	0.41%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	87.80%	7.80%	1.11%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0910817608	C -> DEL	N	N	silent_mutation	Average:44.739; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N
vg0910817608	C -> T	LOC_Os09g17690.1	downstream_gene_variant ; 4163.0bp to feature; MODIFIER	silent_mutation	Average:44.739; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N
vg0910817608	C -> T	LOC_Os09g17680-LOC_Os09g17690	intergenic_region ; MODIFIER	silent_mutation	Average:44.739; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0910817608	NA	7.69E-07	mr1136	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
vg0910817608	NA	2.90E-06	mr1218_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
vg0910817608	5.96E-07	5.96E-07	mr1960_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