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Detailed information for vg0617122838:

Variant ID: vg0617122838 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 17122838
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGATCAATATACTCTCGGCGCATGGACACCCTCTTTTCTGAGGTTTTATTTATCAACCGGTGGAATTTGGCACCTAACGCGGGGCTGCATCGGTTCAGTT[T/C]
GATCTTCGGCGAAGGGGTAAGTCCTATGTTCCATCGGCCCTGGTGAATCTATTAGCTACGTTAGTTGTTCAAGGCTGCATCACTTCGATCTCTTGGATCG

Reverse complement sequence

CGATCCAAGAGATCGAAGTGATGCAGCCTTGAACAACTAACGTAGCTAATAGATTCACCAGGGCCGATGGAACATAGGACTTACCCCTTCGCCGAAGATC[A/G]
AACTGAACCGATGCAGCCCCGCGTTAGGTGCCAAATTCCACCGGTTGATAAATAAAACCTCAGAAAAGAGGGTGTCCATGCGCCGAGAGTATATTGATCG

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	81.80%	17.40%	0.80%	0.00%	NA
All Indica	2759	99.20%	0.60%	0.14%	0.00%	NA
All Japonica	1512	45.20%	52.60%	2.18%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	97.50%	2.50%	0.00%	0.00%	NA
Indica II	465	99.60%	0.00%	0.43%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.50%	0.30%	0.25%	0.00%	NA
Temperate Japonica	767	12.00%	86.40%	1.56%	0.00%	NA
Tropical Japonica	504	91.30%	6.90%	1.79%	0.00%	NA
Japonica Intermediate	241	54.40%	40.70%	4.98%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	88.90%	10.00%	1.11%	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
vg0617122838	T -> C	LOC_Os06g29780-LOC_Os06g29790	intergenic_region ; MODIFIER	silent_mutation	Average:43.885; most accessible tissue: Minghui63 young leaf, score: 59.171	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0617122838	NA	6.00E-22	mr1115	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
vg0617122838	NA	6.56E-12	mr1182	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
vg0617122838	NA	1.11E-06	mr1606	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
vg0617122838	NA	9.14E-13	mr1650	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
vg0617122838	NA	8.10E-10	mr1087_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
vg0617122838	NA	2.47E-06	mr1096_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
vg0617122838	NA	2.84E-07	mr1578_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
vg0617122838	NA	2.14E-06	mr1582_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
vg0617122838	NA	4.10E-06	mr1666_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
vg0617122838	NA	2.97E-06	mr1695_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
vg0617122838	1.76E-07	NA	mr1712_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
vg0617122838	1.51E-06	NA	mr1712_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
vg0617122838	4.95E-06	NA	mr1761_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
vg0617122838	NA	1.98E-06	mr1761_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
vg0617122838	NA	8.74E-06	mr1763_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
vg0617122838	NA	2.00E-08	mr1952_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