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Detailed information for vg0413417765:

Variant ID: vg0413417765 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 13417765
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 336. )

Flanking Sequence (100 bp) in Reference Genome:

GGGAGGGCCAAGATCATAGCCACATCCTGTAGAGTGATGGTCATCTCACCACTGGGAAGATGGAAGCTGTGTGTCTCAGGCCTCCATCTGTCCACAAGTG[C/T]
TGTCAACGCAGGAGCGTTGAACACTGGCATTCCTCTGCTCACGACCAAGGCCACCCCGAGCAACCCGGCCGCCCTTAGGTACGGGATGTACCTATCGTCG

Reverse complement sequence

CGACGATAGGTACATCCCGTACCTAAGGGCGGCCGGGTTGCTCGGGGTGGCCTTGGTCGTGAGCAGAGGAATGCCAGTGTTCAACGCTCCTGCGTTGACA[G/A]
CACTTGTGGACAGATGGAGGCCTGAGACACACAGCTTCCATCTTCCCAGTGGTGAGATGACCATCACTCTACAGGATGTGGCTATGATCTTGGCCCTCCC

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	90.00%	9.70%	0.32%	0.00%	NA
All Indica	2759	99.20%	0.30%	0.47%	0.00%	NA
All Japonica	1512	71.00%	28.80%	0.13%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	98.90%	1.10%	0.00%	0.00%	NA
Indica III	913	99.50%	0.10%	0.44%	0.00%	NA
Indica Intermediate	786	98.50%	0.40%	1.15%	0.00%	NA
Temperate Japonica	767	97.70%	2.30%	0.00%	0.00%	NA
Tropical Japonica	504	25.80%	73.80%	0.40%	0.00%	NA
Japonica Intermediate	241	80.90%	19.10%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	88.90%	11.10%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0413417765	C -> T	LOC_Os04g23470.1	missense_variant ; p.Ala980Thr; MODERATE	nonsynonymous_codon ; A980T	Average:55.111; most accessible tissue: Minghui63 young leaf, score: 73.49	benign	0.383	DELETERIOUS	0.05

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0413417765	NA	2.84E-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
vg0413417765	NA	7.15E-06	mr1213	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
vg0413417765	NA	1.94E-07	mr1338	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
vg0413417765	NA	4.65E-06	mr1425	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
vg0413417765	NA	5.94E-06	mr1425	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
vg0413417765	NA	8.83E-06	mr1982	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
vg0413417765	NA	5.93E-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
vg0413417765	NA	3.14E-07	mr1206_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
vg0413417765	NA	9.23E-07	mr1418_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
vg0413417765	NA	2.07E-06	mr1419_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
vg0413417765	NA	1.67E-06	mr1420_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
vg0413417765	NA	1.44E-06	mr1488_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
vg0413417765	NA	1.30E-06	mr1574_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
vg0413417765	NA	1.15E-07	mr1668_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
vg0413417765	2.70E-06	NA	mr1800_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