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Detailed information for vg0618487881:

Variant ID: vg0618487881 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 18487881
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCATCGTCTTCATCTCCCTCCTGGTAGTAGGCATAGGGATCCTCCGAAGCTTCATCTCCCGTTTCTGATTAATTTTATATTTGCAAGGGTGAGTACCAAC[T/C]
GTACTCAGCAAGCCACCACAGCAACAATGCATATGAAAGGGGTATTTCAAAGGATGGCTATGGCTCTTTTGCGCTAAGCCAGTTTTGTAATTCTTTTCAC

Reverse complement sequence

GTGAAAAGAATTACAAAACTGGCTTAGCGCAAAAGAGCCATAGCCATCCTTTGAAATACCCCTTTCATATGCATTGTTGCTGTGGTGGCTTGCTGAGTAC[A/G]
GTTGGTACTCACCCTTGCAAATATAAAATTAATCAGAAACGGGAGATGAAGCTTCGGAGGATCCCTATGCCTACTACCAGGAGGGAGATGAAGACGATGG

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	40.50%	4.00%	5.16%	50.40%	NA
All Indica	2759	18.80%	0.10%	7.03%	74.05%	NA
All Japonica	1512	86.70%	5.70%	0.33%	7.28%	NA
Aus	269	14.50%	0.00%	15.24%	70.26%	NA
Indica I	595	32.90%	0.00%	3.70%	63.36%	NA
Indica II	465	16.80%	0.00%	5.16%	78.06%	NA
Indica III	913	7.30%	0.20%	10.73%	81.71%	NA
Indica Intermediate	786	22.50%	0.30%	6.36%	70.87%	NA
Temperate Japonica	767	88.30%	6.30%	0.39%	5.08%	NA
Tropical Japonica	504	84.70%	3.40%	0.20%	11.71%	NA
Japonica Intermediate	241	85.90%	8.70%	0.41%	4.98%	NA
VI/Aromatic	96	4.20%	88.50%	0.00%	7.29%	NA
Intermediate	90	44.40%	14.40%	4.44%	36.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0618487881	T -> C	LOC_Os06g31830.1	downstream_gene_variant ; 288.0bp to feature; MODIFIER	silent_mutation	Average:5.711; most accessible tissue: Zhenshan97 flag leaf, score: 10.769	N	N	N	N
vg0618487881	T -> C	LOC_Os06g31830-LOC_Os06g31840	intergenic_region ; MODIFIER	silent_mutation	Average:5.711; most accessible tissue: Zhenshan97 flag leaf, score: 10.769	N	N	N	N
vg0618487881	T -> DEL	N	N	silent_mutation	Average:5.711; most accessible tissue: Zhenshan97 flag leaf, score: 10.769	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0618487881	8.20E-06	NA	mr1550	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
vg0618487881	1.36E-07	NA	mr1281_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
vg0618487881	NA	4.33E-10	mr1829_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
vg0618487881	8.14E-07	1.27E-15	mr1842_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