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Detailed information for vg1018297998:

Variant ID: vg1018297998 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 18297998
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 340. )

Flanking Sequence (100 bp) in Reference Genome:

CTAATCCATTCGTAACAGGTGAGGACATTGCTATTGCTGAGATTGCAATCTCTTCTGTCATTTGTATGGGCATTAACAATAGATGGGATAAGAAATTTAC[A/C]
CAAGAGACCGTTAACTATCTGCAGTTACTTTGGTACGTTAGTCTTACCTAGACTAGATGCTCAATTGGCCAGAATCAAGGGGCCAGGCCCATCTTCAAAA

Reverse complement sequence

TTTTGAAGATGGGCCTGGCCCCTTGATTCTGGCCAATTGAGCATCTAGTCTAGGTAAGACTAACGTACCAAAGTAACTGCAGATAGTTAACGGTCTCTTG[T/G]
GTAAATTTCTTATCCCATCTATTGTTAATGCCCATACAAATGACAGAAGAGATTGCAATCTCAGCAATAGCAATGTCCTCACCTGTTACGAATGGATTAG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	96.30%	3.70%	0.00%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	89.00%	11.00%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.30%	0.00%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	68.10%	31.90%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	97.80%	2.20%	0.00%	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
vg1018297998	A -> C	LOC_Os10g34310.1	3_prime_UTR_variant ; 385.0bp to feature; MODIFIER	silent_mutation	Average:51.246; most accessible tissue: Callus, score: 91.645	N	N	N	N
vg1018297998	A -> C	LOC_Os10g34310.2	3_prime_UTR_variant ; 385.0bp to feature; MODIFIER	silent_mutation	Average:51.246; most accessible tissue: Callus, score: 91.645	N	N	N	N
vg1018297998	A -> C	LOC_Os10g34300.1	upstream_gene_variant ; 800.0bp to feature; MODIFIER	silent_mutation	Average:51.246; most accessible tissue: Callus, score: 91.645	N	N	N	N
vg1018297998	A -> C	LOC_Os10g34290.1	downstream_gene_variant ; 3822.0bp to feature; MODIFIER	silent_mutation	Average:51.246; most accessible tissue: Callus, score: 91.645	N	N	N	N
vg1018297998	A -> C	LOC_Os10g34320.1	downstream_gene_variant ; 3440.0bp to feature; MODIFIER	silent_mutation	Average:51.246; most accessible tissue: Callus, score: 91.645	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1018297998	NA	3.98E-06	mr1600	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