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Detailed information for vg0809155982:

Variant ID: vg0809155982 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 9155982
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGTTGTCCTTGCGATATACGTGTCGGACCTCGATCCCATTAAATCTTTTTTCCAACTTCCTGACTTCTGCGAGATACTTGGACAACTAAGGGCTAGAACA[T/C]
TTGTAATCTTTGTGCACCTGGTTTGCGACTAGTTCGGAATCCCCTTTTACTATCAGTCGCCTGACTCCAAGTGCGGCTGCAGCTCTTATCCCAGCGAGTA

Reverse complement sequence

TACTCGCTGGGATAAGAGCTGCAGCCGCACTTGGAGTCAGGCGACTGATAGTAAAAGGGGATTCCGAACTAGTCGCAAACCAGGTGCACAAAGATTACAA[A/G]
TGTTCTAGCCCTTAGTTGTCCAAGTATCTCGCAGAAGTCAGGAAGTTGGAAAAAAGATTTAATGGGATCGAGGTCCGACACGTATATCGCAAGGACAACA

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	45.40%	26.20%	12.78%	15.64%	NA
All Indica	2759	38.60%	40.30%	13.81%	7.29%	NA
All Japonica	1512	46.00%	6.20%	13.29%	34.59%	NA
Aus	269	96.30%	3.00%	0.74%	0.00%	NA
Indica I	595	40.30%	25.70%	17.31%	16.64%	NA
Indica II	465	39.80%	41.50%	10.54%	8.17%	NA
Indica III	913	34.90%	52.10%	12.05%	0.88%	NA
Indica Intermediate	786	41.00%	36.80%	15.14%	7.12%	NA
Temperate Japonica	767	74.60%	1.60%	4.04%	19.82%	NA
Tropical Japonica	504	7.10%	12.10%	24.21%	56.55%	NA
Japonica Intermediate	241	36.10%	8.30%	19.92%	35.68%	NA
VI/Aromatic	96	83.30%	9.40%	4.17%	3.12%	NA
Intermediate	90	50.00%	18.90%	17.78%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0809155982	T -> C	LOC_Os08g15110.1	upstream_gene_variant ; 424.0bp to feature; MODIFIER	silent_mutation	Average:51.32; most accessible tissue: Zhenshan97 flag leaf, score: 70.007	N	N	N	N
vg0809155982	T -> C	LOC_Os08g15100.1	downstream_gene_variant ; 1591.0bp to feature; MODIFIER	silent_mutation	Average:51.32; most accessible tissue: Zhenshan97 flag leaf, score: 70.007	N	N	N	N
vg0809155982	T -> C	LOC_Os08g15120.1	downstream_gene_variant ; 315.0bp to feature; MODIFIER	silent_mutation	Average:51.32; most accessible tissue: Zhenshan97 flag leaf, score: 70.007	N	N	N	N
vg0809155982	T -> C	LOC_Os08g15110-LOC_Os08g15120	intergenic_region ; MODIFIER	silent_mutation	Average:51.32; most accessible tissue: Zhenshan97 flag leaf, score: 70.007	N	N	N	N
vg0809155982	T -> DEL	N	N	silent_mutation	Average:51.32; most accessible tissue: Zhenshan97 flag leaf, score: 70.007	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0809155982	1.67E-06	1.67E-06	mr1590	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