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Detailed information for vg0620620871:

Variant ID: vg0620620871 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 20620871
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAAGAAGGGGTATATAAAGCTGTGCAACTTTAGTCCCGGTTGGTAACACCAATCGGGCATAAAGATCTCAAATCACTTTAGTCCCGGTTGGTAACACGAA[C/T]
CGAGACTAAAGATCCCAAGCCCCCCGACAGAGGTCTGACATGCCCTGTCAGGAGGTGAACCGGGACTAAAGATGATCTTTAGTCCTGGTTGGTGTTACCA

Reverse complement sequence

TGGTAACACCAACCAGGACTAAAGATCATCTTTAGTCCCGGTTCACCTCCTGACAGGGCATGTCAGACCTCTGTCGGGGGGCTTGGGATCTTTAGTCTCG[G/A]
TTCGTGTTACCAACCGGGACTAAAGTGATTTGAGATCTTTATGCCCGATTGGTGTTACCAACCGGGACTAAAGTTGCACAGCTTTATATACCCCTTCTTC

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	91.10%	0.40%	2.58%	5.95%	NA
All Indica	2759	87.30%	0.10%	3.37%	9.24%	NA
All Japonica	1512	96.60%	1.10%	1.32%	0.99%	NA
Aus	269	97.00%	0.00%	1.86%	1.12%	NA
Indica I	595	78.80%	0.00%	4.54%	16.64%	NA
Indica II	465	83.70%	0.20%	4.30%	11.83%	NA
Indica III	913	95.50%	0.10%	1.53%	2.85%	NA
Indica Intermediate	786	86.40%	0.00%	4.07%	9.54%	NA
Temperate Japonica	767	98.00%	0.10%	0.91%	0.91%	NA
Tropical Japonica	504	93.80%	2.60%	2.18%	1.39%	NA
Japonica Intermediate	241	97.90%	0.80%	0.83%	0.41%	NA
VI/Aromatic	96	97.90%	0.00%	1.04%	1.04%	NA
Intermediate	90	87.80%	1.10%	3.33%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0620620871	C -> T	LOC_Os06g35360.1	upstream_gene_variant ; 598.0bp to feature; MODIFIER	silent_mutation	Average:49.772; most accessible tissue: Zhenshan97 panicle, score: 79.071	N	N	N	N
vg0620620871	C -> T	LOC_Os06g35380.1	upstream_gene_variant ; 4018.0bp to feature; MODIFIER	silent_mutation	Average:49.772; most accessible tissue: Zhenshan97 panicle, score: 79.071	N	N	N	N
vg0620620871	C -> T	LOC_Os06g35370.1	downstream_gene_variant ; 304.0bp to feature; MODIFIER	silent_mutation	Average:49.772; most accessible tissue: Zhenshan97 panicle, score: 79.071	N	N	N	N
vg0620620871	C -> T	LOC_Os06g35360-LOC_Os06g35370	intergenic_region ; MODIFIER	silent_mutation	Average:49.772; most accessible tissue: Zhenshan97 panicle, score: 79.071	N	N	N	N
vg0620620871	C -> DEL	N	N	silent_mutation	Average:49.772; most accessible tissue: Zhenshan97 panicle, score: 79.071	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0620620871	NA	4.57E-06	mr1045	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
vg0620620871	NA	1.05E-07	mr1156	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
vg0620620871	NA	2.80E-07	mr1179	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
vg0620620871	NA	6.58E-06	mr1236	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
vg0620620871	NA	8.36E-08	mr1277	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
vg0620620871	1.11E-06	1.11E-06	mr1663	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
vg0620620871	NA	1.08E-07	mr1746	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