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Detailed information for vg0812109370:

Variant ID: vg0812109370 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 12109370
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, C: 0.02, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:

CATTATAAGCATATTGAATAGGAGCAAAACTAGAAGTAGTATATGCATCTACACAATGATTATTAGCAAAGGACGGATTGGACGAATCGGAGGTTACCTT[T/C]
GGTGAAACTACAACTTGGGGAAGCGAGACATTTCCCTTCACGACGCCTTGATTGTTCCTGATGTATGATTTCATCAACAGCTCCTGCGTAACCACCATCA

Reverse complement sequence

TGATGGTGGTTACGCAGGAGCTGTTGATGAAATCATACATCAGGAACAATCAAGGCGTCGTGAAGGGAAATGTCTCGCTTCCCCAAGTTGTAGTTTCACC[A/G]
AAGGTAACCTCCGATTCGTCCAATCCGTCCTTTGCTAATAATCATTGTGTAGATGCATATACTACTTCTAGTTTTGCTCCTATTCAATATGCTTATAATG

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	50.20%	40.80%	0.72%	8.21%	NA
All Indica	2759	83.40%	7.30%	0.98%	8.34%	NA
All Japonica	1512	2.20%	88.00%	0.13%	9.72%	NA
Aus	269	2.60%	97.00%	0.37%	0.00%	NA
Indica I	595	96.80%	0.30%	0.84%	2.02%	NA
Indica II	465	86.70%	7.70%	1.08%	4.52%	NA
Indica III	913	78.00%	6.90%	0.22%	14.90%	NA
Indica Intermediate	786	77.50%	12.80%	1.91%	7.76%	NA
Temperate Japonica	767	2.00%	97.70%	0.13%	0.26%	NA
Tropical Japonica	504	1.60%	72.40%	0.20%	25.79%	NA
Japonica Intermediate	241	4.10%	89.60%	0.00%	6.22%	NA
VI/Aromatic	96	2.10%	88.50%	2.08%	7.29%	NA
Intermediate	90	35.60%	57.80%	2.22%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0812109370	T -> C	LOC_Os08g20180.1	synonymous_variant ; p.Pro55Pro; LOW	synonymous_codon	Average:64.173; most accessible tissue: Minghui63 panicle, score: 76.913	N	N	N	N
vg0812109370	T -> DEL	LOC_Os08g20180.1	N	frameshift_variant	Average:64.173; most accessible tissue: Minghui63 panicle, score: 76.913	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0812109370	NA	3.00E-08	mr1134	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
vg0812109370	NA	8.66E-08	mr1135	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
vg0812109370	NA	1.27E-20	mr1422	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
vg0812109370	NA	3.88E-07	mr1504	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
vg0812109370	NA	2.31E-16	mr1583	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
vg0812109370	NA	3.60E-18	mr1598	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
vg0812109370	NA	4.66E-16	mr1870	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
vg0812109370	NA	1.26E-06	mr1134_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
vg0812109370	NA	8.80E-13	mr1134_2	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
vg0812109370	NA	1.59E-24	mr1422_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
vg0812109370	NA	1.26E-10	mr1504_2	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
vg0812109370	NA	7.41E-08	mr1672_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
vg0812109370	NA	1.40E-11	mr1850_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