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Detailed information for vg1113821400:

Variant ID: vg1113821400 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 13821400
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.01, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:

TGCAGGAAGCTGCATTACAAGCAATTGTGTATTACCGACATTATAGGCCAGGGTTGGACGGGTTCTTTCATTTCTTTCCAGCTCGCGCAAACCAATCCTC[C/T]
GCTAATTACTATCCAGGTCTTGAGGGAAACATGAGAGAGATTGACACTCCAGGACTATTCTTAGCTGGCCTGGTTCGTGCTATGGATAGATATCTCGCAA

Reverse complement sequence

TTGCGAGATATCTATCCATAGCACGAACCAGGCCAGCTAAGAATAGTCCTGGAGTGTCAATCTCTCTCATGTTTCCCTCAAGACCTGGATAGTAATTAGC[G/A]
GAGGATTGGTTTGCGCGAGCTGGAAAGAAATGAAAGAACCCGTCCAACCCTGGCCTATAATGTCGGTAATACACAATTGCTTGTAATGCAGCTTCCTGCA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	81.90%	8.50%	1.18%	8.44%	NA
All Indica	2759	71.10%	14.10%	1.52%	13.27%	NA
All Japonica	1512	99.00%	0.00%	0.00%	0.99%	NA
Aus	269	92.60%	1.90%	3.72%	1.86%	NA
Indica I	595	91.60%	3.40%	0.84%	4.20%	NA
Indica II	465	57.00%	23.40%	2.80%	16.77%	NA
Indica III	913	64.10%	19.30%	1.64%	15.01%	NA
Indica Intermediate	786	72.30%	10.60%	1.15%	16.03%	NA
Temperate Japonica	767	98.60%	0.00%	0.00%	1.43%	NA
Tropical Japonica	504	99.60%	0.00%	0.00%	0.40%	NA
Japonica Intermediate	241	99.20%	0.00%	0.00%	0.83%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	72.20%	8.90%	4.44%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1113821400	C -> T	LOC_Os11g24260.1	synonymous_variant ; p.Ser34Ser; LOW	synonymous_codon	Average:8.838; most accessible tissue: Minghui63 root, score: 17.665	N	N	N	N
vg1113821400	C -> DEL	LOC_Os11g24260.1	N	frameshift_variant	Average:8.838; most accessible tissue: Minghui63 root, score: 17.665	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1113821400	3.92E-06	3.92E-06	mr1852	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