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Detailed information for vg1117719367:

Variant ID: vg1117719367 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 17719367
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:

TCATTGGCTCGCTGATTTACCTGGCTAGTGCAACTAGGCCTGATATCTCCTTTGCTGTCAGCATGGTGAGCCGGTTTACCTCTAATCCGGGAGATGATCA[C/T]
TGGCGTGCGCTTGAGCGAGTAATGCGCTATCTGAAAGGTACTATGGAATTAGGGCTTCACTATTCTGGGTATCCTGCGGTACTGGAGGGATATAGTGATT

Reverse complement sequence

AATCACTATATCCCTCCAGTACCGCAGGATACCCAGAATAGTGAAGCCCTAATTCCATAGTACCTTTCAGATAGCGCATTACTCGCTCAAGCGCACGCCA[G/A]
TGATCATCTCCCGGATTAGAGGTAAACCGGCTCACCATGCTGACAGCAAAGGAGATATCAGGCCTAGTTGCACTAGCCAGGTAAATCAGCGAGCCAATGA

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	74.70%	9.60%	14.64%	1.08%	NA
All Indica	2759	69.30%	4.30%	24.54%	1.81%	NA
All Japonica	1512	78.20%	21.50%	0.26%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	50.10%	3.00%	42.86%	4.03%	NA
Indica II	465	81.70%	1.50%	16.34%	0.43%	NA
Indica III	913	73.40%	6.20%	18.73%	1.64%	NA
Indica Intermediate	786	71.90%	4.70%	22.26%	1.15%	NA
Temperate Japonica	767	98.80%	1.00%	0.13%	0.00%	NA
Tropical Japonica	504	42.50%	57.30%	0.20%	0.00%	NA
Japonica Intermediate	241	87.60%	11.60%	0.83%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	75.60%	11.10%	12.22%	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
vg1117719367	C -> T	LOC_Os11g30470.1	synonymous_variant ; p.His981His; LOW	synonymous_codon	Average:36.715; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg1117719367	C -> DEL	LOC_Os11g30470.1	N	frameshift_variant	Average:36.715; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1117719367	9.86E-06	NA	mr1115_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
vg1117719367	6.33E-06	NA	mr1241_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
vg1117719367	NA	1.61E-06	mr1248_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
vg1117719367	NA	6.84E-06	mr1263_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
vg1117719367	NA	8.95E-06	mr1289_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
vg1117719367	NA	7.63E-08	mr1418_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
vg1117719367	NA	2.52E-07	mr1419_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
vg1117719367	NA	1.52E-07	mr1420_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
vg1117719367	NA	9.81E-06	mr1440_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
vg1117719367	4.33E-06	6.37E-08	mr1467_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
vg1117719367	NA	3.83E-07	mr1488_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
vg1117719367	NA	9.05E-06	mr1492_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
vg1117719367	NA	3.35E-06	mr1556_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
vg1117719367	NA	2.01E-07	mr1567_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
vg1117719367	8.55E-06	NA	mr1611_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
vg1117719367	NA	7.16E-06	mr1759_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
vg1117719367	NA	4.18E-06	mr1764_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
vg1117719367	NA	3.49E-06	mr1811_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
vg1117719367	NA	4.35E-06	mr1812_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
vg1117719367	NA	8.97E-06	mr1816_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