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Detailed information for vg1119906028:

Variant ID: vg1119906028 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 19906028
Reference Allele: C	Alternative Allele: G
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, C: 0.00, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

AAGGCAGAGGAGGTGGCTAGAGTTGATTAAAGACTATGATCTTAACATTCAATACACACCGGGTAAGGCGAATGTGGTTGCAGATGCTCTAAGCCGTAAG[C/G]
TCGTTCCTCCAACTGTGAGTTGTTTGATAACTGATTTTGAACGGATGGATATCTCCTATTGTTATGTTGGAGTGGCAAGTACCGAGTCACGAGTCATTCT

Reverse complement sequence

AGAATGACTCGTGACTCGGTACTTGCCACTCCAACATAACAATAGGAGATATCCATCCGTTCAAAATCAGTTATCAAACAACTCACAGTTGGAGGAACGA[G/C]
CTTACGGCTTAGAGCATCTGCAACCACATTCGCCTTACCCGGTGTGTATTGAATGTTAAGATCATAGTCTTTAATCAACTCTAGCCACCTCCTCTGCCTT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	55.40%	21.90%	7.77%	15.02%	NA
All Indica	2759	84.10%	4.60%	6.38%	4.93%	NA
All Japonica	1512	5.10%	53.40%	3.84%	37.63%	NA
Aus	269	62.80%	0.40%	36.80%	0.00%	NA
Indica I	595	96.50%	1.30%	2.02%	0.17%	NA
Indica II	465	90.10%	4.10%	5.81%	0.00%	NA
Indica III	913	76.20%	5.30%	8.11%	10.41%	NA
Indica Intermediate	786	80.20%	6.70%	8.02%	5.09%	NA
Temperate Japonica	767	6.50%	81.00%	0.65%	11.86%	NA
Tropical Japonica	504	3.60%	22.00%	9.13%	65.28%	NA
Japonica Intermediate	241	3.70%	31.50%	2.90%	61.83%	NA
VI/Aromatic	96	6.20%	66.70%	26.04%	1.04%	NA
Intermediate	90	50.00%	35.60%	10.00%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1119906028	C -> DEL	LOC_Os11g34050.1	N	frameshift_variant	Average:7.608; most accessible tissue: Zhenshan97 root, score: 12.891	N	N	N	N
vg1119906028	C -> G	LOC_Os11g34050.1	missense_variant ; p.Leu597Val; MODERATE	nonsynonymous_codon ; L597V	Average:7.608; most accessible tissue: Zhenshan97 root, score: 12.891	unknown	unknown	TOLERATED	0.37

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1119906028	NA	1.44E-07	mr1179	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
vg1119906028	NA	2.83E-10	mr1549	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
vg1119906028	NA	4.63E-08	mr1729	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
vg1119906028	NA	1.25E-09	mr1757	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
vg1119906028	NA	8.10E-09	mr1864	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
vg1119906028	NA	4.68E-08	mr1156_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
vg1119906028	NA	6.51E-06	mr1549_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
vg1119906028	NA	4.55E-09	mr1741_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
vg1119906028	NA	2.76E-11	mr1746_2	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
vg1119906028	NA	2.80E-07	mr1757_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