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Detailed information for vg1017951405:

Variant ID: vg1017951405 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 17951405
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

AAAGCGGTGGAATTGAGATAATATGTTCAATACTGCTCCAAATTCAGGAAATTACCTTTGACTACAAGAAAATTTCCCTTCGAATGGTTGTACATTGACA[G/A]
CACGAACACTGCATTCATGGTGTAATCTGGCTTAAAGCTTAGTCGGGACAGCACAAGAGAAAGAGCAACATGTGGAGTTCCATCACCAAGGGTTTTATGC

Reverse complement sequence

GCATAAAACCCTTGGTGATGGAACTCCACATGTTGCTCTTTCTCTTGTGCTGTCCCGACTAAGCTTTAAGCCAGATTACACCATGAATGCAGTGTTCGTG[C/T]
TGTCAATGTACAACCATTCGAAGGGAAATTTTCTTGTAGTCAAAGGTAATTTCCTGAATTTGGAGCAGTATTGAACATATTATCTCAATTCCACCGCTTT

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	90.10%	2.60%	3.98%	3.28%	NA
All Indica	2759	98.10%	0.00%	1.09%	0.83%	NA
All Japonica	1512	90.80%	8.20%	0.93%	0.07%	NA
Aus	269	6.30%	0.00%	47.96%	45.72%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	98.90%	0.00%	0.65%	0.43%	NA
Indica III	913	97.70%	0.00%	1.31%	0.99%	NA
Indica Intermediate	786	96.60%	0.00%	1.91%	1.53%	NA
Temperate Japonica	767	84.00%	14.70%	1.30%	0.00%	NA
Tropical Japonica	504	99.20%	0.00%	0.60%	0.20%	NA
Japonica Intermediate	241	95.00%	4.60%	0.41%	0.00%	NA
VI/Aromatic	96	78.10%	0.00%	14.58%	7.29%	NA
Intermediate	90	97.80%	0.00%	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
vg1017951405	G -> A	LOC_Os10g33830.1	synonymous_variant ; p.Leu209Leu; LOW	synonymous_codon	Average:36.155; most accessible tissue: Callus, score: 51.315	N	N	N	N
vg1017951405	G -> DEL	LOC_Os10g33830.1	N	frameshift_variant	Average:36.155; most accessible tissue: Callus, score: 51.315	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1017951405	NA	4.28E-06	mr1210	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
vg1017951405	9.20E-07	9.19E-07	mr1346	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
vg1017951405	2.33E-06	1.27E-06	mr1379	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
vg1017951405	NA	5.97E-06	mr1428	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
vg1017951405	2.01E-06	2.01E-06	mr1456	Jap_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
vg1017951405	NA	4.37E-07	mr1515	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
vg1017951405	4.85E-06	4.85E-06	mr1577	Jap_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
vg1017951405	2.35E-06	1.25E-09	mr1585	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
vg1017951405	NA	1.83E-07	mr1586	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
vg1017951405	NA	3.14E-08	mr1765	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
vg1017951405	7.67E-07	2.13E-08	mr1780	Jap_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
vg1017951405	NA	1.90E-07	mr1585_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
vg1017951405	NA	6.19E-07	mr1765_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