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Detailed information for vg1101519635:

Variant ID: vg1101519635 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 1519635
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAAATGCACTTAATAGCTCTAGGCTCCAATTTACCATTATCAACATGAGCATAAGCAGTACAGCCAAATACTCTTAAGTCTGAATAATTTGCTGGGGAAC[T/C]
AGACCATACCTCAATTGGAGTCTTCTTATCAATGGCATAACTAGGTGATCGATTGATAAGATAACAAGCAGTGGAAACGGCTTCCGCCCAAAACTGTTTA

Reverse complement sequence

TAAACAGTTTTGGGCGGAAGCCGTTTCCACTGCTTGTTATCTTATCAATCGATCACCTAGTTATGCCATTGATAAGAAGACTCCAATTGAGGTATGGTCT[A/G]
GTTCCCCAGCAAATTATTCAGACTTAAGAGTATTTGGCTGTACTGCTTATGCTCATGTTGATAATGGTAAATTGGAGCCTAGAGCTATTAAGTGCATTTT

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	33.80%	2.00%	3.98%	60.24%	NA
All Indica	2759	2.10%	1.80%	2.54%	93.55%	NA
All Japonica	1512	96.20%	0.00%	0.00%	3.77%	NA
Aus	269	0.70%	14.50%	39.03%	45.72%	NA
Indica I	595	2.50%	1.00%	2.35%	94.12%	NA
Indica II	465	1.90%	0.20%	1.51%	96.34%	NA
Indica III	913	1.40%	2.80%	2.08%	93.65%	NA
Indica Intermediate	786	2.70%	2.20%	3.82%	91.35%	NA
Temperate Japonica	767	97.10%	0.00%	0.00%	2.87%	NA
Tropical Japonica	504	95.60%	0.00%	0.00%	4.37%	NA
Japonica Intermediate	241	94.60%	0.00%	0.00%	5.39%	NA
VI/Aromatic	96	39.60%	0.00%	10.42%	50.00%	NA
Intermediate	90	50.00%	4.40%	3.33%	42.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1101519635	T -> DEL	N	N	silent_mutation	Average:5.821; most accessible tissue: Callus, score: 14.497	N	N	N	N
vg1101519635	T -> C	LOC_Os11g03840.1	downstream_gene_variant ; 2388.0bp to feature; MODIFIER	silent_mutation	Average:5.821; most accessible tissue: Callus, score: 14.497	N	N	N	N
vg1101519635	T -> C	LOC_Os11g03830.1	intron_variant ; MODIFIER	silent_mutation	Average:5.821; most accessible tissue: Callus, score: 14.497	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1101519635	NA	1.58E-08	mr1779	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