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Detailed information for vg0519167025:

Variant ID: vg0519167025 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 19167025
Reference Allele: A	Alternative Allele: C
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 340. )

Flanking Sequence (100 bp) in Reference Genome:

TAAGAGGCAAACTTCATTGCCTTCCCCAGAAATACTGAGATGACGGATTAAAGTATTGTATGTGATAACGGTAGCTACAAACTCTTTGCTTCTCAGCAGA[A/C]
AAAGCGCTTTATGAAGTCTCCCCAATTTACAGAGGCTGTGGACAACAATGTTGAAGGTCCAGCTATTTGGAGCAATGCCTTTCTTGGCCATGTCAGTGAA

Reverse complement sequence

TTCACTGACATGGCCAAGAAAGGCATTGCTCCAAATAGCTGGACCTTCAACATTGTTGTCCACAGCCTCTGTAAATTGGGGAGACTTCATAAAGCGCTTT[T/G]
TCTGCTGAGAAGCAAAGAGTTTGTAGCTACCGTTATCACATACAATACTTTAATCCGTCATCTCAGTATTTCTGGGGAAGGCAATGAAGTTTGCCTCTTA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	69.90%	30.00%	0.02%	0.06%	NA
All Indica	2759	99.20%	0.80%	0.00%	0.04%	NA
All Japonica	1512	15.30%	84.60%	0.00%	0.07%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	99.10%	0.90%	0.00%	0.00%	NA
Indica III	913	99.20%	0.80%	0.00%	0.00%	NA
Indica Intermediate	786	98.70%	1.10%	0.00%	0.13%	NA
Temperate Japonica	767	5.20%	94.80%	0.00%	0.00%	NA
Tropical Japonica	504	31.20%	68.70%	0.00%	0.20%	NA
Japonica Intermediate	241	14.50%	85.50%	0.00%	0.00%	NA
VI/Aromatic	96	8.30%	91.70%	0.00%	0.00%	NA
Intermediate	90	67.80%	30.00%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0519167025	A -> DEL	LOC_Os05g32730.1	N	frameshift_variant	Average:59.539; most accessible tissue: Callus, score: 81.032	N	N	N	N
vg0519167025	A -> C	LOC_Os05g32730.1	missense_variant ; p.Phe404Cys; MODERATE	nonsynonymous_codon ; F404C	Average:59.539; most accessible tissue: Callus, score: 81.032	unknown	unknown	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0519167025	NA	1.35E-09	mr1277	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
vg0519167025	9.66E-06	NA	mr1301	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
vg0519167025	3.75E-07	NA	mr1410	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
vg0519167025	NA	1.49E-07	mr1676	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
vg0519167025	NA	7.45E-33	mr1733	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
vg0519167025	3.17E-07	NA	mr1410_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
vg0519167025	NA	1.03E-06	mr1629_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
vg0519167025	NA	2.38E-07	mr1676_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