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Detailed information for vg0605892046:

Variant ID: vg0605892046 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 5892046
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.86, T: 0.12, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:

TACTTAGATCCACAATCAACTGATTGAAGACGTCCACGTGCATCCTAAGATCTGACTCCTCTTGCATCTGCAAACCATACAGCTGTTGTTTGAGATACAA[T/C]
TTACTCGTTAGCGACTTGGACATATACAGGTTTGCCAACTTGTCCCAAATTTCCTTCGGTGATTTTTCGTCCATGACCTGGTACATGACAGAATCCGAGA

Reverse complement sequence

TCTCGGATTCTGTCATGTACCAGGTCATGGACGAAAAATCACCGAAGGAAATTTGGGACAAGTTGGCAAACCTGTATATGTCCAAGTCGCTAACGAGTAA[A/G]
TTGTATCTCAAACAACAGCTGTATGGTTTGCAGATGCAAGAGGAGTCAGATCTTAGGATGCACGTGGACGTCTTCAATCAGTTGATTGTGGATCTAAGTA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	63.30%	36.60%	0.11%	0.00%	NA
All Indica	2759	65.30%	34.60%	0.07%	0.00%	NA
All Japonica	1512	75.40%	24.50%	0.07%	0.00%	NA
Aus	269	1.50%	98.50%	0.00%	0.00%	NA
Indica I	595	90.90%	9.10%	0.00%	0.00%	NA
Indica II	465	41.50%	58.30%	0.22%	0.00%	NA
Indica III	913	60.50%	39.50%	0.00%	0.00%	NA
Indica Intermediate	786	65.60%	34.20%	0.13%	0.00%	NA
Temperate Japonica	767	99.10%	0.90%	0.00%	0.00%	NA
Tropical Japonica	504	41.90%	57.90%	0.20%	0.00%	NA
Japonica Intermediate	241	70.10%	29.90%	0.00%	0.00%	NA
VI/Aromatic	96	0.00%	100.00%	0.00%	0.00%	NA
Intermediate	90	48.90%	48.90%	2.22%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0605892046	T -> C	LOC_Os06g11220.1	synonymous_variant ; p.Lys46Lys; LOW	synonymous_codon	Average:44.345; most accessible tissue: Zhenshan97 root, score: 64.819	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0605892046	NA	2.41E-06	mr1308	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
vg0605892046	NA	1.95E-08	mr1530	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
vg0605892046	NA	2.19E-08	mr1570	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
vg0605892046	NA	1.11E-08	mr1593	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
vg0605892046	NA	5.04E-08	mr1304_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
vg0605892046	1.56E-06	1.56E-06	mr1581_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
vg0605892046	NA	1.13E-06	mr1819_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
vg0605892046	NA	8.47E-06	mr1851_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
vg0605892046	NA	2.15E-09	mr1864_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