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Detailed information for vg1122020161:

Variant ID: vg1122020161 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 22020161
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.92, C: 0.08, others allele: 0.00, population size: 38. )

Flanking Sequence (100 bp) in Reference Genome:

TTATGGTGCTATATTTTTTATAAAAAAATAGTCGGCATGTATTTACATTGTAAGTCCCTAAATTACATATGTAATTTTAGTGTATTTACAATGTAAGTCT[T/C]
AAAATTACATATGTAATGTAAATTTGAAAATTACATACTAATTACATATATAAGTGAGGTGTAAATGAGGTGTAACTACTGCGTAAGTGGCTGAAAAAAA

Reverse complement sequence

TTTTTTTCAGCCACTTACGCAGTAGTTACACCTCATTTACACCTCACTTATATATGTAATTAGTATGTAATTTTCAAATTTACATTACATATGTAATTTT[A/G]
AGACTTACATTGTAAATACACTAAAATTACATATGTAATTTAGGGACTTACAATGTAAATACATGCCGACTATTTTTTTATAAAAAATATAGCACCATAA

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	27.00%	18.50%	10.20%	44.24%	NA
All Indica	2759	27.80%	1.30%	8.08%	62.85%	NA
All Japonica	1512	22.30%	54.40%	14.02%	9.33%	NA
Aus	269	54.30%	1.90%	11.15%	32.71%	NA
Indica I	595	42.90%	1.50%	24.71%	30.92%	NA
Indica II	465	28.40%	1.10%	2.15%	68.39%	NA
Indica III	913	18.90%	0.80%	2.30%	77.98%	NA
Indica Intermediate	786	26.20%	1.90%	5.73%	66.16%	NA
Temperate Japonica	767	9.90%	74.10%	12.39%	3.65%	NA
Tropical Japonica	504	42.10%	23.00%	17.46%	17.46%	NA
Japonica Intermediate	241	20.30%	57.30%	12.03%	10.37%	NA
VI/Aromatic	96	5.20%	0.00%	3.12%	91.67%	NA
Intermediate	90	25.60%	14.40%	15.56%	44.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1122020161	T -> DEL	N	N	silent_mutation	Average:48.071; most accessible tissue: Zhenshan97 panicle, score: 79.799	N	N	N	N
vg1122020161	T -> C	LOC_Os11g37280.1	downstream_gene_variant ; 1622.0bp to feature; MODIFIER	silent_mutation	Average:48.071; most accessible tissue: Zhenshan97 panicle, score: 79.799	N	N	N	N
vg1122020161	T -> C	LOC_Os11g37290.1	intron_variant ; MODIFIER	silent_mutation	Average:48.071; most accessible tissue: Zhenshan97 panicle, score: 79.799	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1122020161	NA	3.24E-06	mr1156	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
vg1122020161	NA	3.53E-06	mr1380	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
vg1122020161	NA	1.61E-07	mr1629	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
vg1122020161	NA	4.55E-06	mr1780	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
vg1122020161	NA	8.77E-06	mr1826	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
vg1122020161	1.24E-06	2.44E-09	mr1982	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
vg1122020161	NA	7.28E-07	mr1679_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
vg1122020161	NA	2.05E-06	mr1980_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