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Detailed information for vg1009691370:

Variant ID: vg1009691370 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 9691370
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: 291. )

Flanking Sequence (100 bp) in Reference Genome:

ATATCTCAAATCCTTGGCATATCTCTTCTCAGCATCTGTTGGTCTCGTCTTGTTGTTCCTTGAGGCTGTTCCTTGGCCTCGCGCTCTCTGCCCTCTGCTT[C/T]
AGCTTCTTCCGTTGACATGAGGGCTAGAACGAGATGACTCTCAGAGATACACTCACGAAACTCTCCAACTCCAAGTCCAAGAGCTTGACGAACTTGTCAA

Reverse complement sequence

TTGACAAGTTCGTCAAGCTCTTGGACTTGGAGTTGGAGAGTTTCGTGAGTGTATCTCTGAGAGTCATCTCGTTCTAGCCCTCATGTCAACGGAAGAAGCT[G/A]
AAGCAGAGGGCAGAGAGCGCGAGGCCAAGGAACAGCCTCAAGGAACAACAAGACGAGACCAACAGATGCTGAGAAGAGATATGCCAAGGATTTGAGATAT

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	64.20%	27.60%	0.34%	7.83%	NA
All Indica	2759	60.90%	38.60%	0.04%	0.43%	NA
All Japonica	1512	63.40%	12.30%	0.93%	23.35%	NA
Aus	269	98.50%	1.50%	0.00%	0.00%	NA
Indica I	595	75.00%	25.00%	0.00%	0.00%	NA
Indica II	465	41.90%	57.80%	0.00%	0.22%	NA
Indica III	913	65.10%	33.70%	0.00%	1.20%	NA
Indica Intermediate	786	56.60%	43.30%	0.13%	0.00%	NA
Temperate Japonica	767	75.60%	1.00%	0.65%	22.69%	NA
Tropical Japonica	504	35.70%	31.20%	1.79%	31.35%	NA
Japonica Intermediate	241	82.60%	8.70%	0.00%	8.71%	NA
VI/Aromatic	96	77.10%	22.90%	0.00%	0.00%	NA
Intermediate	90	64.40%	28.90%	1.11%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1009691370	C -> T	LOC_Os10g19030.1	synonymous_variant ; p.Phe82Phe; LOW	synonymous_codon	Average:63.589; most accessible tissue: Zhenshan97 young leaf, score: 84.814	N	N	N	N
vg1009691370	C -> DEL	LOC_Os10g19030.1	N	frameshift_variant	Average:63.589; most accessible tissue: Zhenshan97 young leaf, score: 84.814	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1009691370	2.03E-06	2.65E-10	mr1053	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
vg1009691370	4.95E-07	4.87E-07	mr1053	Ind_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
vg1009691370	4.62E-06	NA	mr1070	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
vg1009691370	2.46E-06	NA	mr1070	Ind_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
vg1009691370	5.04E-07	NA	mr1128	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
vg1009691370	3.29E-07	5.18E-07	mr1128	Ind_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
vg1009691370	8.16E-07	NA	mr1147	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
vg1009691370	2.90E-06	4.35E-06	mr1147	Ind_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
vg1009691370	NA	8.80E-13	mr1709	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
vg1009691370	NA	7.09E-10	mr1709	Ind_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
vg1009691370	NA	1.13E-08	mr1027_2	Ind_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
vg1009691370	NA	8.50E-07	mr1053_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
vg1009691370	7.45E-06	1.58E-06	mr1053_2	Ind_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
vg1009691370	NA	5.84E-08	mr1250_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
vg1009691370	NA	1.76E-09	mr1709_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
vg1009691370	NA	1.49E-09	mr1709_2	Ind_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