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Detailed information for vg1111162952:

Variant ID: vg1111162952 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 11162952
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACCCTCGTCGCGGAGGAGCCCGTGACTACGCCACCTTCAGGGATGCTAGCTCGGAGGATGACGCTACCATCATGCACCTGGCACGCATGGTGGAGGCGTA[T/C]
GACGCAGCCCGTATCGACTTCCATCATATGGTGCGCCGTGGGTTGGTCGAGAACAACATGAAGATCCTGGAGCTGCGTCAGGAGAATCTGCAGCTGAAGA

Reverse complement sequence

TCTTCAGCTGCAGATTCTCCTGACGCAGCTCCAGGATCTTCATGTTGTTCTCGACCAACCCACGGCGCACCATATGATGGAAGTCGATACGGGCTGCGTC[A/G]
TACGCCTCCACCATGCGTGCCAGGTGCATGATGGTAGCGTCATCCTCCGAGCTAGCATCCCTGAAGGTGGCGTAGTCACGGGCTCCTCCGCGACGAGGGT

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	37.80%	0.70%	19.55%	41.90%	NA
All Indica	2759	6.90%	1.00%	24.07%	68.10%	NA
All Japonica	1512	96.10%	0.10%	1.19%	2.65%	NA
Aus	269	4.80%	1.50%	82.16%	11.52%	NA
Indica I	595	5.90%	0.50%	10.42%	83.19%	NA
Indica II	465	4.10%	1.30%	22.80%	71.83%	NA
Indica III	913	5.80%	1.10%	34.61%	58.49%	NA
Indica Intermediate	786	10.40%	1.00%	22.90%	65.65%	NA
Temperate Japonica	767	96.90%	0.00%	1.04%	2.09%	NA
Tropical Japonica	504	94.20%	0.00%	1.59%	4.17%	NA
Japonica Intermediate	241	97.50%	0.40%	0.83%	1.24%	NA
VI/Aromatic	96	90.60%	0.00%	7.29%	2.08%	NA
Intermediate	90	51.10%	2.20%	15.56%	31.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1111162952	T -> DEL	LOC_Os11g19410.1	N	frameshift_variant	Average:16.947; most accessible tissue: Callus, score: 33.92	N	N	N	N
vg1111162952	T -> C	LOC_Os11g19410.1	synonymous_variant ; p.Tyr212Tyr; LOW	synonymous_codon	Average:16.947; most accessible tissue: Callus, score: 33.92	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1111162952	NA	5.49E-87	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
vg1111162952	1.01E-07	2.14E-07	mr1295_2	Ind_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