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Detailed information for vg0402221936:

Variant ID: vg0402221936 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 2221936
Reference Allele: G	Alternative Allele: C
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, G: 0.05, others allele: 0.00, population size: 93. )

Flanking Sequence (100 bp) in Reference Genome:

GTCATATGTGGAAAGGACTATTTTGTAATATTAAAACACATGAAAGAAAGAGTAGGTACAAACATGAAGGAGTTGTTAGTAAAATATTCTTTTAAAAGGA[G/C]
TAAATAATAGATAGAAATAATTGAAAGCGCATATGAAAATACAGTTGCAGATTTGCTACAAACTCTTCCTATTATTTCTCACATCTTATCATTTTTAAAT

Reverse complement sequence

ATTTAAAAATGATAAGATGTGAGAAATAATAGGAAGAGTTTGTAGCAAATCTGCAACTGTATTTTCATATGCGCTTTCAATTATTTCTATCTATTATTTA[C/G]
TCCTTTTAAAAGAATATTTTACTAACAACTCCTTCATGTTTGTACCTACTCTTTCTTTCATGTGTTTTAATATTACAAAATAGTCCTTTCCACATATGAC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	64.20%	24.50%	0.63%	10.66%	NA
All Indica	2759	75.80%	17.50%	0.29%	6.42%	NA
All Japonica	1512	39.70%	42.70%	1.32%	16.34%	NA
Aus	269	85.10%	3.00%	0.74%	11.15%	NA
Indica I	595	92.80%	5.50%	0.17%	1.51%	NA
Indica II	465	95.70%	3.00%	0.22%	1.08%	NA
Indica III	913	58.30%	31.10%	0.33%	10.30%	NA
Indica Intermediate	786	71.50%	19.30%	0.38%	8.78%	NA
Temperate Japonica	767	31.80%	63.20%	2.09%	2.87%	NA
Tropical Japonica	504	59.70%	13.70%	0.79%	25.79%	NA
Japonica Intermediate	241	22.80%	37.80%	0.00%	39.42%	NA
VI/Aromatic	96	41.70%	11.50%	0.00%	46.88%	NA
Intermediate	90	80.00%	14.40%	0.00%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0402221936	G -> C	LOC_Os04g04640.1	intron_variant ; MODIFIER	silent_mutation	Average:23.366; most accessible tissue: Callus, score: 29.855	N	N	N	N
vg0402221936	G -> DEL	N	N	silent_mutation	Average:23.366; most accessible tissue: Callus, score: 29.855	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0402221936	NA	9.58E-07	mr1164	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
vg0402221936	NA	5.22E-12	mr1182	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
vg0402221936	NA	4.55E-06	mr1182	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
vg0402221936	NA	9.67E-11	mr1244	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
vg0402221936	NA	3.26E-06	mr1330	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
vg0402221936	NA	4.73E-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
vg0402221936	NA	8.74E-09	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
vg0402221936	NA	1.15E-06	mr1708	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
vg0402221936	NA	9.57E-07	mr1748	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
vg0402221936	NA	3.08E-06	mr1077_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
vg0402221936	NA	3.05E-07	mr1229_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
vg0402221936	NA	1.15E-07	mr1521_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
vg0402221936	NA	7.63E-07	mr1745_2	Ind_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
vg0402221936	NA	2.92E-08	mr1880_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