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Detailed information for vg1124078018:

Variant ID: vg1124078018 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24078018
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TACATGAATTTCTGAAGATCGAGCAGCAGGTGGACTAGAGCTGACTGTGTCCTGAACATGGGTAGACACATCACTGCTCTGATTAGATGGTCCAGGAGTG[C/T]
TGTTCCTGAAATTTGCACTCTTCTGCTGTTGCCATAATTTGCTCTTCTCGATGCCACAGTGGCAAAACAAAGCCCAGATGACGGTTACGAACTCGACACC

Reverse complement sequence

GGTGTCGAGTTCGTAACCGTCATCTGGGCTTTGTTTTGCCACTGTGGCATCGAGAAGAGCAAATTATGGCAACAGCAGAAGAGTGCAAATTTCAGGAACA[G/A]
CACTCCTGGACCATCTAATCAGAGCAGTGATGTGTCTACCCATGTTCAGGACACAGTCAGCTCTAGTCCACCTGCTGCTCGATCTTCAGAAATTCATGTA

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	37.90%	17.60%	0.89%	43.63%	NA
All Indica	2759	32.90%	2.80%	1.30%	62.96%	NA
All Japonica	1512	45.90%	40.40%	0.20%	13.49%	NA
Aus	269	23.80%	44.60%	1.12%	30.48%	NA
Indica I	595	5.00%	2.20%	1.68%	91.09%	NA
Indica II	465	27.10%	1.90%	0.22%	70.75%	NA
Indica III	913	54.80%	1.10%	1.10%	43.04%	NA
Indica Intermediate	786	32.20%	5.70%	1.91%	60.18%	NA
Temperate Japonica	767	39.40%	52.90%	0.13%	7.56%	NA
Tropical Japonica	504	52.80%	33.30%	0.00%	13.89%	NA
Japonica Intermediate	241	52.30%	15.40%	0.83%	31.54%	NA
VI/Aromatic	96	86.50%	1.00%	0.00%	12.50%	NA
Intermediate	90	44.40%	25.60%	0.00%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1124078018	C -> T	LOC_Os11g40390.1	missense_variant ; p.Ser393Asn; MODERATE	nonsynonymous_codon ; S393N	Average:20.029; most accessible tissue: Callus, score: 86.44	unknown	unknown	TOLERATED	1.00
vg1124078018	C -> DEL	LOC_Os11g40390.1	N	frameshift_variant	Average:20.029; most accessible tissue: Callus, score: 86.44	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124078018	4.41E-06	NA	mr1088_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
vg1124078018	4.45E-06	NA	mr1131_2	Ind_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
vg1124078018	2.75E-06	NA	mr1199_2	Ind_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
vg1124078018	4.86E-06	NA	mr1246_2	Ind_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
vg1124078018	NA	5.08E-06	mr1407_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
vg1124078018	4.33E-06	3.72E-06	mr1595_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
vg1124078018	NA	2.34E-06	mr1600_2	Ind_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
vg1124078018	5.93E-06	2.64E-06	mr1609_2	Ind_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
vg1124078018	5.07E-06	NA	mr1763_2	Ind_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
vg1124078018	3.87E-08	3.87E-08	mr1852_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
vg1124078018	NA	6.77E-06	mr1888_2	Ind_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
vg1124078018	6.86E-07	1.63E-06	mr1909_2	Ind_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