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Detailed information for vg0504619344:

Variant ID: vg0504619344 (JBrowse)	Variation Type: INDEL
Chromosome: chr05	Position: 4619344
Reference Allele: A	Alternative Allele: G,AG
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.04, others allele: 0.00, population size: 159. )

Flanking Sequence (100 bp) in Reference Genome:

TTTCTTTTGTTTTTTCGATATAACTGTCAAGTAGATATCACGTCTGCACATATGAGACTAAGTTAATGTCACGTCAACGAAAACCGTTCTCCAAAAAAGG[A/G,AG]
AGTAATTTTGTATGGTTATGTTCTCAAAACAATAATGGGAGTACTTAGAGGACTCGGCATATTCGATATTCGGTTTTGCGTTTGCGGTTATGGCTTTCAC

Reverse complement sequence

GTGAAAGCCATAACCGCAAACGCAAAACCGAATATCGAATATGCCGAGTCCTCTAAGTACTCCCATTATTGTTTTGAGAACATAACCATACAAAATTACT[T/C,CT]
CCTTTTTTGGAGAACGGTTTTCGTTGACGTGACATTAACTTAGTCTCATATGTGCAGACGTGATATCTACTTGACAGTTATATCGAAAAAACAAAAGAAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	67.80%	31.20%	0.15%	0.00%	AG: 0.89%
All Indica	2759	97.80%	2.00%	0.11%	0.00%	AG: 0.11%
All Japonica	1512	11.20%	88.50%	0.13%	0.00%	AG: 0.20%
Aus	269	84.80%	2.60%	0.00%	0.00%	AG: 12.64%
Indica I	595	99.50%	0.50%	0.00%	0.00%	NA
Indica II	465	95.10%	4.70%	0.22%	0.00%	NA
Indica III	913	99.10%	0.70%	0.11%	0.00%	AG: 0.11%
Indica Intermediate	786	96.40%	3.20%	0.13%	0.00%	AG: 0.25%
Temperate Japonica	767	2.30%	97.70%	0.00%	0.00%	NA
Tropical Japonica	504	26.20%	73.20%	0.20%	0.00%	AG: 0.40%
Japonica Intermediate	241	7.90%	91.30%	0.41%	0.00%	AG: 0.41%
VI/Aromatic	96	68.80%	31.20%	0.00%	0.00%	NA
Intermediate	90	48.90%	46.70%	2.22%	0.00%	AG: 2.22%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0504619344	A -> AG	LOC_Os05g08450.1	downstream_gene_variant ; 4043.0bp to feature; MODIFIER	silent_mutation	Average:75.672; most accessible tissue: Callus, score: 96.294	N	N	N	N
vg0504619344	A -> AG	LOC_Os05g08460.1	downstream_gene_variant ; 2216.0bp to feature; MODIFIER	silent_mutation	Average:75.672; most accessible tissue: Callus, score: 96.294	N	N	N	N
vg0504619344	A -> AG	LOC_Os05g08450-LOC_Os05g08460	intergenic_region ; MODIFIER	silent_mutation	Average:75.672; most accessible tissue: Callus, score: 96.294	N	N	N	N
vg0504619344	A -> G	LOC_Os05g08450.1	downstream_gene_variant ; 4042.0bp to feature; MODIFIER	silent_mutation	Average:75.672; most accessible tissue: Callus, score: 96.294	N	N	N	N
vg0504619344	A -> G	LOC_Os05g08460.1	downstream_gene_variant ; 2217.0bp to feature; MODIFIER	silent_mutation	Average:75.672; most accessible tissue: Callus, score: 96.294	N	N	N	N
vg0504619344	A -> G	LOC_Os05g08450-LOC_Os05g08460	intergenic_region ; MODIFIER	silent_mutation	Average:75.672; most accessible tissue: Callus, score: 96.294	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0504619344	NA	1.15E-19	mr1021	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
vg0504619344	NA	2.97E-67	mr1027	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
vg0504619344	NA	5.59E-26	mr1076	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
vg0504619344	NA	8.62E-40	mr1082	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
vg0504619344	NA	1.13E-31	mr1086	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
vg0504619344	NA	9.77E-59	mr1103	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
vg0504619344	NA	8.22E-31	mr1107	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
vg0504619344	NA	1.18E-38	mr1139	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
vg0504619344	NA	4.89E-27	mr1145	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
vg0504619344	NA	3.41E-30	mr1204	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
vg0504619344	NA	1.30E-31	mr1226	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
vg0504619344	NA	5.89E-15	mr1228	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
vg0504619344	NA	9.26E-63	mr1246	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
vg0504619344	NA	2.85E-15	mr1324	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
vg0504619344	NA	3.63E-11	mr1325	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
vg0504619344	NA	6.28E-14	mr1326	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
vg0504619344	NA	3.37E-14	mr1361	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
vg0504619344	NA	1.48E-26	mr1411	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
vg0504619344	NA	3.50E-28	mr1436	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
vg0504619344	NA	5.80E-41	mr1437	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
vg0504619344	NA	1.37E-46	mr1558	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
vg0504619344	NA	1.09E-12	mr1744	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
vg0504619344	NA	3.77E-52	mr1070_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
vg0504619344	NA	3.09E-37	mr1082_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
vg0504619344	NA	1.57E-35	mr1083_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
vg0504619344	NA	2.72E-34	mr1085_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
vg0504619344	NA	1.64E-78	mr1088_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
vg0504619344	NA	1.63E-72	mr1103_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
vg0504619344	NA	1.07E-41	mr1104_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
vg0504619344	NA	3.26E-38	mr1107_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
vg0504619344	NA	5.31E-36	mr1129_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
vg0504619344	NA	3.72E-47	mr1145_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
vg0504619344	NA	4.21E-38	mr1155_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
vg0504619344	NA	1.09E-37	mr1181_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
vg0504619344	NA	1.09E-17	mr1199_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
vg0504619344	NA	2.64E-38	mr1224_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
vg0504619344	NA	4.49E-44	mr1226_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
vg0504619344	NA	1.97E-26	mr1233_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
vg0504619344	NA	7.00E-40	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
vg0504619344	NA	1.29E-78	mr1246_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
vg0504619344	NA	3.51E-44	mr1264_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
vg0504619344	NA	1.07E-25	mr1350_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
vg0504619344	NA	5.46E-62	mr1402_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
vg0504619344	NA	2.14E-54	mr1404_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
vg0504619344	NA	5.67E-51	mr1437_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
vg0504619344	NA	2.04E-60	mr1599_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
vg0504619344	NA	1.46E-51	mr1620_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
vg0504619344	NA	1.56E-15	mr1686_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
vg0504619344	NA	3.07E-38	mr1878_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
vg0504619344	NA	2.58E-34	mr1888_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
vg0504619344	NA	2.31E-25	mr1949_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