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Detailed information for vg1122958019:

Variant ID: vg1122958019 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 22958019
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGGGGAGGGAGCCCGTCATGGCTCTCTCGCGGCCGGATCCGCCGCCCGCGGCCCAGCAGCGGTCGCGTCGTCGTCGCGGCAGCCTCCCCCATAGTAGCGG[T/C]
AGTGGATCCGACCTCCCCTGTCATGGTGGCTGCAGATCGGGCTTCCCCCGTCATCACGATGCCGGATCCGGCCTCCCCCGTCGTCGTGGCGGCTGGATCC

Reverse complement sequence

GGATCCAGCCGCCACGACGACGGGGGAGGCCGGATCCGGCATCGTGATGACGGGGGAAGCCCGATCTGCAGCCACCATGACAGGGGAGGTCGGATCCACT[A/G]
CCGCTACTATGGGGGAGGCTGCCGCGACGACGACGCGACCGCTGCTGGGCCGCGGGCGGCGGATCCGGCCGCGAGAGAGCCATGACGGGCTCCCTCCCCG

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	73.40%	23.90%	0.02%	2.71%	NA
All Indica	2759	98.90%	1.00%	0.00%	0.11%	NA
All Japonica	1512	20.50%	71.20%	0.07%	8.20%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	99.50%	0.50%	0.00%	0.00%	NA
Indica II	465	98.90%	0.90%	0.00%	0.22%	NA
Indica III	913	98.80%	1.20%	0.00%	0.00%	NA
Indica Intermediate	786	98.50%	1.30%	0.00%	0.25%	NA
Temperate Japonica	767	17.20%	79.80%	0.00%	3.00%	NA
Tropical Japonica	504	20.60%	62.50%	0.20%	16.67%	NA
Japonica Intermediate	241	30.70%	62.20%	0.00%	7.05%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	75.60%	23.30%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1122958019	T -> DEL	LOC_Os11g38680.1	N	frameshift_variant	Average:67.355; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N
vg1122958019	T -> C	LOC_Os11g38680.1	synonymous_variant ; p.Gly130Gly; LOW	synonymous_codon	Average:67.355; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1122958019	NA	1.95E-08	mr1020_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
vg1122958019	NA	5.48E-06	mr1066_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
vg1122958019	1.26E-06	NA	mr1127_2	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
vg1122958019	NA	6.37E-07	mr1153_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
vg1122958019	NA	1.01E-08	mr1198_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
vg1122958019	NA	8.66E-11	mr1232_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
vg1122958019	NA	5.55E-06	mr1262_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
vg1122958019	NA	2.90E-07	mr1275_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
vg1122958019	NA	9.21E-06	mr1407_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
vg1122958019	NA	7.21E-06	mr1462_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
vg1122958019	NA	9.03E-17	mr1557_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
vg1122958019	NA	1.03E-15	mr1575_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
vg1122958019	NA	7.13E-11	mr1714_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
vg1122958019	NA	6.07E-16	mr1726_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
vg1122958019	NA	1.91E-10	mr1765_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
vg1122958019	NA	4.35E-06	mr1869_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
vg1122958019	NA	1.19E-08	mr1909_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
vg1122958019	NA	8.08E-08	mr1921_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
vg1122958019	NA	2.02E-19	mr1922_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
vg1122958019	NA	2.12E-09	mr1940_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
vg1122958019	4.33E-06	5.27E-19	mr1980_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