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Detailed information for vg0402105567:

Variant ID: vg0402105567 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 2105567
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCCCAACGCCACCTTCACGTGATGAGAGGTTATCTATTAGTAATCAACCTAAGTAGCAACTTGCGGAATGTACGAGTCAAAAATCATATATTACATCGAG[T/C]
ATACCTTGATTGATAAGTTCTTGAAGGGAATATGCAGCTCACATGGTGTCCGTTGCGTGATCTCATCAACGGGGCAGGTGGTTTCGTCCTGGGTTTGCAT

Reverse complement sequence

ATGCAAACCCAGGACGAAACCACCTGCCCCGTTGATGAGATCACGCAACGGACACCATGTGAGCTGCATATTCCCTTCAAGAACTTATCAATCAAGGTAT[A/G]
CTCGATGTAATATATGATTTTTGACTCGTACATTCCGCAAGTTGCTACTTAGGTTGATTACTAATAGATAACCTCTCATCACGTGAAGGTGGCGTTGGGA

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	30.00%	2.10%	31.49%	36.37%	NA
All Indica	2759	19.70%	3.40%	44.87%	32.00%	NA
All Japonica	1512	54.20%	0.10%	2.18%	43.52%	NA
Aus	269	4.80%	0.70%	61.34%	33.09%	NA
Indica I	595	16.60%	3.00%	46.55%	33.78%	NA
Indica II	465	11.60%	2.40%	26.24%	59.78%	NA
Indica III	913	24.60%	4.70%	54.87%	15.77%	NA
Indica Intermediate	786	21.00%	2.90%	43.00%	33.08%	NA
Temperate Japonica	767	87.20%	0.00%	0.39%	12.39%	NA
Tropical Japonica	504	18.50%	0.20%	3.97%	77.38%	NA
Japonica Intermediate	241	24.10%	0.00%	4.15%	71.78%	NA
VI/Aromatic	96	12.50%	1.00%	35.42%	51.04%	NA
Intermediate	90	35.60%	0.00%	20.00%	44.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0402105567	T -> C	LOC_Os04g04410.1	upstream_gene_variant ; 4309.0bp to feature; MODIFIER	silent_mutation	Average:6.983; most accessible tissue: Callus, score: 17.867	N	N	N	N
vg0402105567	T -> C	LOC_Os04g04430.1	downstream_gene_variant ; 4162.0bp to feature; MODIFIER	silent_mutation	Average:6.983; most accessible tissue: Callus, score: 17.867	N	N	N	N
vg0402105567	T -> C	LOC_Os04g04420.1	intron_variant ; MODIFIER	silent_mutation	Average:6.983; most accessible tissue: Callus, score: 17.867	N	N	N	N
vg0402105567	T -> DEL	N	N	silent_mutation	Average:6.983; most accessible tissue: Callus, score: 17.867	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0402105567	NA	2.24E-12	mr1034	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
vg0402105567	2.61E-06	2.61E-06	mr1666	Ind_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
vg0402105567	NA	7.05E-07	mr1785	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
vg0402105567	NA	1.72E-06	mr1211_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
vg0402105567	NA	3.97E-07	mr1671_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