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Detailed information for vg1108425600:

Variant ID: vg1108425600 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 8425600
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTCCTCCCCTTCGCAATGGCAGGGCTGGTTCCGCCATTTTCTTCTTTCTTTATGGATGTTCTGGATTTCTACGATCTCCAGATGGCGCACCTCACCCCT[A/C]
ATGCAGTGATGACATTGGCCATCTTCACGCACCTGTGCGAGATGTTCATTGGGGTGCGCCCATCTCTTCGGCTGTTCCGGTGGTTCTTCACCGTGCAGTC

Reverse complement sequence

GACTGCACGGTGAAGAACCACCGGAACAGCCGAAGAGATGGGCGCACCCCAATGAACATCTCGCACAGGTGCGTGAAGATGGCCAATGTCATCACTGCAT[T/G]
AGGGGTGAGGTGCGCCATCTGGAGATCGTAGAAATCCAGAACATCCATAAAGAAAGAAGAAAATGGCGGAACCAGCCCTGCCATTGCGAAGGGGAGGAAA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	46.20%	4.10%	30.62%	19.09%	NA
All Indica	2759	21.50%	0.60%	48.89%	29.07%	NA
All Japonica	1512	92.10%	0.00%	3.11%	4.83%	NA
Aus	269	25.30%	61.30%	10.04%	3.35%	NA
Indica I	595	10.10%	0.20%	42.52%	47.23%	NA
Indica II	465	16.10%	0.20%	55.27%	28.39%	NA
Indica III	913	28.40%	0.30%	53.89%	17.42%	NA
Indica Intermediate	786	25.20%	1.40%	44.15%	29.26%	NA
Temperate Japonica	767	94.30%	0.00%	1.30%	4.43%	NA
Tropical Japonica	504	90.90%	0.00%	4.56%	4.56%	NA
Japonica Intermediate	241	87.60%	0.00%	5.81%	6.64%	NA
VI/Aromatic	96	88.50%	9.40%	1.04%	1.04%	NA
Intermediate	90	53.30%	2.20%	25.56%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1108425600	A -> DEL	LOC_Os11g14960.1	N	frameshift_variant	Average:13.59; most accessible tissue: Minghui63 root, score: 21.615	N	N	N	N
vg1108425600	A -> C	LOC_Os11g14960.1	missense_variant ; p.Asn92His; MODERATE	nonsynonymous_codon	Average:13.59; most accessible tissue: Minghui63 root, score: 21.615	probably damaging	2.743	DELETERIOUS	0.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1108425600	NA	2.39E-06	mr1006	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
vg1108425600	NA	8.77E-07	mr1052	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
vg1108425600	NA	2.31E-06	mr1262	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
vg1108425600	NA	5.74E-08	mr1403	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
vg1108425600	NA	2.11E-06	mr1415	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
vg1108425600	NA	4.13E-06	mr1417	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
vg1108425600	NA	6.65E-06	mr1545	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
vg1108425600	NA	1.87E-06	mr1556	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
vg1108425600	NA	2.11E-06	mr1567	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
vg1108425600	NA	9.05E-06	mr1774	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
vg1108425600	NA	7.53E-08	mr1347_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
vg1108425600	NA	2.06E-06	mr1743_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
vg1108425600	3.39E-06	NA	mr1922_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