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Detailed information for vg0409773871:

Variant ID: vg0409773871 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 9773871
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTTTTGTCAATTAATGCCAATATTGACATATATTGGCACACGTGGGTGTGAAGTTTTTCACCGGAATGCAAAAGTTCAAAAACCACCAAAAAATGATATT[C/T]
GGACATATTGGGGTATATTGGGTGCGTTCGTGGCAAAAACTCACTTCGTGAATCGTGCGGCGAACTTTTGTCAATTAATGCCAATATTGGCACACGTGGG

Reverse complement sequence

CCCACGTGTGCCAATATTGGCATTAATTGACAAAAGTTCGCCGCACGATTCACGAAGTGAGTTTTTGCCACGAACGCACCCAATATACCCCAATATGTCC[G/A]
AATATCATTTTTTGGTGGTTTTTGAACTTTTGCATTCCGGTGAAAAACTTCACACCCACGTGTGCCAATATATGTCAATATTGGCATTAATTGACAAAAG

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	27.40%	0.80%	23.61%	48.20%	NA
All Indica	2759	8.00%	1.20%	20.70%	70.10%	NA
All Japonica	1512	68.10%	0.20%	29.43%	2.31%	NA
Aus	269	1.90%	0.40%	1.86%	95.91%	NA
Indica I	595	19.50%	0.30%	24.03%	56.13%	NA
Indica II	465	7.10%	0.90%	15.27%	76.77%	NA
Indica III	913	0.90%	2.60%	22.23%	74.26%	NA
Indica Intermediate	786	8.30%	0.30%	19.59%	71.88%	NA
Temperate Japonica	767	96.90%	0.00%	2.35%	0.78%	NA
Tropical Japonica	504	21.20%	0.40%	74.01%	4.37%	NA
Japonica Intermediate	241	74.30%	0.40%	22.41%	2.90%	NA
VI/Aromatic	96	9.40%	1.00%	76.04%	13.54%	NA
Intermediate	90	33.30%	0.00%	24.44%	42.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0409773871	C -> DEL	N	N	silent_mutation	Average:12.778; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0409773871	C -> T	LOC_Os04g17830.1	upstream_gene_variant ; 1829.0bp to feature; MODIFIER	silent_mutation	Average:12.778; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0409773871	C -> T	LOC_Os04g17820.1	downstream_gene_variant ; 3394.0bp to feature; MODIFIER	silent_mutation	Average:12.778; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0409773871	C -> T	LOC_Os04g17820-LOC_Os04g17830	intergenic_region ; MODIFIER	silent_mutation	Average:12.778; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0409773871	NA	1.29E-06	mr1090	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
vg0409773871	NA	2.65E-06	mr1121	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
vg0409773871	NA	1.29E-07	mr1194	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
vg0409773871	NA	4.00E-68	mr1489	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
vg0409773871	NA	2.35E-12	mr1650	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
vg0409773871	NA	1.21E-08	mr1658	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
vg0409773871	NA	1.45E-17	mr1768	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
vg0409773871	NA	1.32E-44	mr1771	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
vg0409773871	NA	2.25E-73	mr1778	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
vg0409773871	NA	1.18E-35	mr1784	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
vg0409773871	NA	6.69E-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
vg0409773871	NA	6.76E-31	mr1789	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
vg0409773871	NA	4.58E-10	mr1790	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
vg0409773871	NA	4.60E-24	mr1805	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
vg0409773871	NA	2.65E-14	mr1982	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
vg0409773871	NA	2.93E-71	mr1019_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
vg0409773871	NA	1.65E-08	mr1090_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
vg0409773871	NA	9.34E-50	mr1093_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
vg0409773871	4.96E-06	4.95E-06	mr1111_2	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
vg0409773871	NA	6.41E-08	mr1121_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
vg0409773871	NA	3.43E-06	mr1144_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
vg0409773871	NA	2.82E-07	mr1194_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
vg0409773871	NA	2.41E-07	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
vg0409773871	NA	8.06E-52	mr1235_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
vg0409773871	NA	1.66E-39	mr1243_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
vg0409773871	NA	6.12E-13	mr1248_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
vg0409773871	NA	1.15E-06	mr1248_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
vg0409773871	NA	7.00E-08	mr1399_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
vg0409773871	NA	6.18E-76	mr1489_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
vg0409773871	NA	1.13E-39	mr1771_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
vg0409773871	NA	1.72E-74	mr1778_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
vg0409773871	NA	3.93E-45	mr1784_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
vg0409773871	NA	1.08E-28	mr1789_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