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Detailed information for vg1109919219:

Variant ID: vg1109919219 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 9919219
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGTACCACTGTACCCACAAGACACAGCCCCACAATATGTCACCATGCGCCGCAATACCACCACGGTACCTCGGAAAGGAGCTGTGACAGTACCCCTCGCA[T/C]
AACACAATCCACCACAACGCACCATTCCTTGATCATAATCACCCCCTTATAAACAAGGCATGGACTCCCCAGCGACCCCCGTGGGCTTATCTCCGCCACT

Reverse complement sequence

AGTGGCGGAGATAAGCCCACGGGGGTCGCTGGGGAGTCCATGCCTTGTTTATAAGGGGGTGATTATGATCAAGGAATGGTGCGTTGTGGTGGATTGTGTT[A/G]
TGCGAGGGGTACTGTCACAGCTCCTTTCCGAGGTACCGTGGTGGTATTGCGGCGCATGGTGACATATTGTGGGGCTGTGTCTTGTGGGTACAGTGGTACA

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	52.10%	0.10%	14.49%	33.24%	NA
All Indica	2759	23.70%	0.10%	23.74%	52.41%	NA
All Japonica	1512	97.00%	0.10%	0.40%	2.58%	NA
Aus	269	92.20%	0.00%	1.86%	5.95%	NA
Indica I	595	33.40%	0.00%	20.50%	46.05%	NA
Indica II	465	16.10%	0.00%	12.47%	71.40%	NA
Indica III	913	14.30%	0.00%	36.14%	49.51%	NA
Indica Intermediate	786	31.80%	0.40%	18.45%	49.36%	NA
Temperate Japonica	767	97.50%	0.10%	0.13%	2.22%	NA
Tropical Japonica	504	96.20%	0.00%	0.60%	3.17%	NA
Japonica Intermediate	241	96.70%	0.00%	0.83%	2.49%	NA
VI/Aromatic	96	44.80%	2.10%	12.50%	40.62%	NA
Intermediate	90	57.80%	0.00%	7.78%	34.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1109919219	T -> DEL	N	N	silent_mutation	Average:11.546; most accessible tissue: Callus, score: 21.583	N	N	N	N
vg1109919219	T -> C	LOC_Os11g17740.1	downstream_gene_variant ; 1253.0bp to feature; MODIFIER	silent_mutation	Average:11.546; most accessible tissue: Callus, score: 21.583	N	N	N	N
vg1109919219	T -> C	LOC_Os11g17740-LOC_Os11g17760	intergenic_region ; MODIFIER	silent_mutation	Average:11.546; most accessible tissue: Callus, score: 21.583	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1109919219	NA	5.10E-11	mr1188	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
vg1109919219	NA	4.70E-11	mr1188_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