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Detailed information for vg1124810339:

Variant ID: vg1124810339 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24810339
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.79, T: 0.22, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

AGCCGAGCGGCGACGACGACGGCTTCACGGCGACGACGAACGGGGGGCCCTCGACGGTGATGTCGCACCGGATGGTGAACCCGTCGTCCCTGACGCACCA[T/C]
GGCGACATGTCCAGCTTCTCCGTCGAGATGAAGCGCTGGAAGCCGAAGCTGGAGTCCGGCCAGAACGTGCACCTGAACCTGCCGGCGACCTCCGTCTCCG

Reverse complement sequence

CGGAGACGGAGGTCGCCGGCAGGTTCAGGTGCACGTTCTGGCCGGACTCCAGCTTCGGCTTCCAGCGCTTCATCTCGACGGAGAAGCTGGACATGTCGCC[A/G]
TGGTGCGTCAGGGACGACGGGTTCACCATCCGGTGCGACATCACCGTCGAGGGCCCCCCGTTCGTCGTCGCCGTGAAGCCGTCGTCGTCGCCGCTCGGCT

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	78.50%	21.30%	0.02%	0.23%	NA
All Indica	2759	87.70%	11.80%	0.04%	0.40%	NA
All Japonica	1512	60.80%	39.20%	0.00%	0.00%	NA
Aus	269	98.10%	1.90%	0.00%	0.00%	NA
Indica I	595	76.10%	23.20%	0.00%	0.67%	NA
Indica II	465	93.10%	6.50%	0.22%	0.22%	NA
Indica III	913	92.70%	6.90%	0.00%	0.44%	NA
Indica Intermediate	786	87.70%	12.10%	0.00%	0.25%	NA
Temperate Japonica	767	51.80%	48.20%	0.00%	0.00%	NA
Tropical Japonica	504	65.10%	34.90%	0.00%	0.00%	NA
Japonica Intermediate	241	80.90%	19.10%	0.00%	0.00%	NA
VI/Aromatic	96	33.30%	66.70%	0.00%	0.00%	NA
Intermediate	90	80.00%	20.00%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1124810339	T -> DEL	LOC_Os11g41350.1	N	frameshift_variant	Average:57.77; most accessible tissue: Zhenshan97 young leaf, score: 79.225	N	N	N	N
vg1124810339	T -> C	LOC_Os11g41350.1	synonymous_variant ; p.Pro160Pro; LOW	synonymous_codon	Average:57.77; most accessible tissue: Zhenshan97 young leaf, score: 79.225	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124810339	9.79E-06	9.79E-06	mr1319	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
vg1124810339	NA	5.94E-07	mr1332	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
vg1124810339	NA	3.13E-06	mr1330_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
vg1124810339	NA	2.49E-06	mr1332_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
vg1124810339	3.62E-07	3.62E-07	mr1579_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