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Detailed information for vg0408184131:

Variant ID: vg0408184131 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 8184131
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:

GTGCCCGTTGCCGAAGATGGAGGAGCGCCATCTGCTTCCGCACCTGTGCTATCACTACCGCCTTCGGCCCCTACCACCTCTGTGCAGGTGCCGAACGCGG[C/T]
CGACATGACGAAGGCTGCTGCGGCGGCAAGGGCACTCCAGACCAGGGCGGAGATCCTTTCGACAAGCCAATTGTTGGTGCCACAAGACGCTCCATCGCAG

Reverse complement sequence

CTGCGATGGAGCGTCTTGTGGCACCAACAATTGGCTTGTCGAAAGGATCTCCGCCCTGGTCTGGAGTGCCCTTGCCGCCGCAGCAGCCTTCGTCATGTCG[G/A]
CCGCGTTCGGCACCTGCACAGAGGTGGTAGGGGCCGAAGGCGGTAGTGATAGCACAGGTGCGGAAGCAGATGGCGCTCCTCCATCTTCGGCAACGGGCAC

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	46.40%	13.80%	15.85%	23.99%	NA
All Indica	2759	40.40%	3.20%	24.32%	32.08%	NA
All Japonica	1512	64.40%	29.20%	2.71%	3.64%	NA
Aus	269	21.60%	9.70%	7.06%	61.71%	NA
Indica I	595	45.70%	1.00%	25.55%	27.73%	NA
Indica II	465	47.70%	2.60%	16.56%	33.12%	NA
Indica III	913	32.20%	3.60%	31.22%	32.97%	NA
Indica Intermediate	786	41.60%	4.70%	19.97%	33.72%	NA
Temperate Japonica	767	96.30%	2.10%	0.78%	0.78%	NA
Tropical Japonica	504	12.50%	77.00%	4.96%	5.56%	NA
Japonica Intermediate	241	71.40%	15.80%	4.15%	8.71%	NA
VI/Aromatic	96	8.30%	78.10%	7.29%	6.25%	NA
Intermediate	90	41.10%	22.20%	12.22%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0408184131	C -> DEL	N	N	silent_mutation	Average:25.991; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg0408184131	C -> T	LOC_Os04g14590.1	upstream_gene_variant ; 2133.0bp to feature; MODIFIER	silent_mutation	Average:25.991; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg0408184131	C -> T	LOC_Os04g14580.1	intron_variant ; MODIFIER	silent_mutation	Average:25.991; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0408184131	NA	9.50E-07	mr1082	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
vg0408184131	NA	5.49E-06	mr1083	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
vg0408184131	2.34E-06	NA	mr1086	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
vg0408184131	NA	1.87E-06	mr1226	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
vg0408184131	6.78E-08	6.33E-07	mr1233	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
vg0408184131	NA	8.75E-06	mr1236_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
vg0408184131	8.83E-07	8.27E-09	mr1498_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