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Detailed information for vg1113607448:

Variant ID: vg1113607448 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 13607448
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAGCCCGCGACTACGCCACCTTCAGGGATGTTAGCTCGGAGGATGACGCTACCATCATGCACCTAGCGCGCATGGTGGAGGCGTACGACGCGGCCCGTAT[T/C]
GACTTCCATCGTATGGTGTGCTGTGGGTTGGTCGAGAACAACATGAAGATCCTGGAGCTGCGTCAGGAGAATTTGCAGCTGAAGAAGGACTTGGACGCGG

Reverse complement sequence

CCGCGTCCAAGTCCTTCTTCAGCTGCAAATTCTCCTGACGCAGCTCCAGGATCTTCATGTTGTTCTCGACCAACCCACAGCACACCATACGATGGAAGTC[A/G]
ATACGGGCCGCGTCGTACGCCTCCACCATGCGCGCTAGGTGCATGATGGTAGCGTCATCCTCCGAGCTAACATCCCTGAAGGTGGCGTAGTCGCGGGCTC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	46.00%	0.10%	19.72%	34.15%	NA
All Indica	2759	20.10%	0.10%	26.64%	53.10%	NA
All Japonica	1512	95.80%	0.00%	0.66%	3.51%	NA
Aus	269	15.60%	0.00%	61.71%	22.68%	NA
Indica I	595	20.70%	0.00%	13.78%	65.55%	NA
Indica II	465	18.90%	0.40%	27.10%	53.55%	NA
Indica III	913	19.30%	0.00%	34.17%	46.55%	NA
Indica Intermediate	786	21.40%	0.30%	27.35%	51.02%	NA
Temperate Japonica	767	97.30%	0.00%	0.13%	2.61%	NA
Tropical Japonica	504	92.70%	0.00%	1.39%	5.95%	NA
Japonica Intermediate	241	97.90%	0.00%	0.83%	1.24%	NA
VI/Aromatic	96	91.70%	0.00%	4.17%	4.17%	NA
Intermediate	90	45.60%	1.10%	18.89%	34.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1113607448	T -> DEL	LOC_Os11g24006.1	N	frameshift_variant	Average:16.079; most accessible tissue: Callus, score: 49.805	N	N	N	N
vg1113607448	T -> C	LOC_Os11g24006.1	synonymous_variant ; p.Ile203Ile; LOW	synonymous_codon	Average:16.079; most accessible tissue: Callus, score: 49.805	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1113607448	NA	6.61E-15	mr1376	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
vg1113607448	NA	9.89E-23	mr1383	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
vg1113607448	NA	6.61E-15	mr1431	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
vg1113607448	NA	1.20E-11	mr1636	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
vg1113607448	7.94E-06	2.56E-90	mr1758	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
vg1113607448	NA	1.33E-10	mr1775	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
vg1113607448	NA	5.68E-07	mr1797	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
vg1113607448	NA	5.68E-07	mr1801	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
vg1113607448	NA	1.49E-14	mr1162_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
vg1113607448	3.01E-06	NA	mr1758_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
vg1113607448	NA	4.59E-09	mr1758_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
vg1113607448	NA	1.02E-07	mr1913_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