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Detailed information for vg0402081771:

Variant ID: vg0402081771 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 2081771
Reference Allele: C	Alternative Allele: A
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.91, A: 0.10, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:

GCAGGCACCCTGAACGATTTGTACCATGCTATGATATGCAGAGACAAGCGAGGAAGAACAGCAAGCAAACATCCAACACCAATTAACTGGCCATCCATTA[C/A]
CAGGGAGAAAATGTATAAGGAGGAAGAAATCACACCAGGCATACAGATTTGGCACTGAGATAGAAAGAGCATCGATTCAATACCAAATCAGGGGGGCAAA

Reverse complement sequence

TTTGCCCCCCTGATTTGGTATTGAATCGATGCTCTTTCTATCTCAGTGCCAAATCTGTATGCCTGGTGTGATTTCTTCCTCCTTATACATTTTCTCCCTG[G/T]
TAATGGATGGCCAGTTAATTGGTGTTGGATGTTTGCTTGCTGTTCTTCCTCGCTTGTCTCTGCATATCATAGCATGGTACAAATCGTTCAGGGTGCCTGC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	52.60%	35.40%	0.42%	11.57%	NA
All Indica	2759	79.60%	19.10%	0.18%	1.16%	NA
All Japonica	1512	14.80%	56.60%	0.60%	27.98%	NA
Aus	269	4.50%	83.60%	0.74%	11.15%	NA
Indica I	595	84.40%	15.50%	0.17%	0.00%	NA
Indica II	465	94.20%	5.40%	0.00%	0.43%	NA
Indica III	913	69.80%	28.00%	0.11%	2.08%	NA
Indica Intermediate	786	78.80%	19.50%	0.38%	1.40%	NA
Temperate Japonica	767	1.40%	73.10%	0.78%	24.64%	NA
Tropical Japonica	504	38.50%	34.70%	0.20%	26.59%	NA
Japonica Intermediate	241	7.90%	49.80%	0.83%	41.49%	NA
VI/Aromatic	96	6.20%	38.50%	2.08%	53.12%	NA
Intermediate	90	55.60%	30.00%	2.22%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0402081771	C -> DEL	N	N	silent_mutation	Average:57.956; most accessible tissue: Callus, score: 77.97	N	N	N	N
vg0402081771	C -> A	LOC_Os04g04390.1	intron_variant ; MODIFIER	silent_mutation	Average:57.956; most accessible tissue: Callus, score: 77.97	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0402081771	1.92E-06	1.75E-33	mr1037	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
vg0402081771	NA	2.89E-06	mr1037	Ind_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
vg0402081771	NA	1.93E-37	mr1094	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
vg0402081771	NA	5.37E-17	mr1147	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
vg0402081771	NA	5.42E-16	mr1199	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
vg0402081771	NA	4.46E-21	mr1422	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
vg0402081771	NA	1.05E-11	mr1540	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
vg0402081771	NA	1.07E-10	mr1720	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
vg0402081771	5.47E-11	2.89E-64	mr1798	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
vg0402081771	NA	6.48E-07	mr1798	Ind_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
vg0402081771	4.45E-06	2.59E-08	mr1798	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
vg0402081771	9.99E-06	9.29E-33	mr1037_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
vg0402081771	NA	7.33E-49	mr1091_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
vg0402081771	NA	2.34E-45	mr1094_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
vg0402081771	NA	5.60E-54	mr1108_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
vg0402081771	NA	9.32E-50	mr1111_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
vg0402081771	NA	3.45E-53	mr1121_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
vg0402081771	NA	3.04E-08	mr1126_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
vg0402081771	NA	2.20E-51	mr1144_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
vg0402081771	NA	8.11E-14	mr1147_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
vg0402081771	NA	1.55E-27	mr1270_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
vg0402081771	NA	4.48E-06	mr1439_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
vg0402081771	NA	2.00E-10	mr1649_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
vg0402081771	NA	3.93E-08	mr1690_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
vg0402081771	NA	1.03E-15	mr1720_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
vg0402081771	NA	6.36E-11	mr1734_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
vg0402081771	NA	3.50E-15	mr1744_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
vg0402081771	6.53E-16	1.81E-90	mr1798_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
vg0402081771	NA	3.23E-11	mr1798_2	Ind_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
vg0402081771	1.71E-09	5.53E-14	mr1798_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
vg0402081771	NA	2.42E-06	mr1834_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
vg0402081771	2.95E-06	NA	mr1879_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
vg0402081771	NA	9.62E-06	mr1896_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
vg0402081771	NA	1.44E-07	mr1991_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