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Detailed information for vg1018461662:

Variant ID: vg1018461662 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 18461662
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.62, T: 0.37, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

TGAAAGAGGTTAGCGGCGAAGTCAGCCCGAACACCCCCGACATTAGCTCGGAGGTCACCGAGGTAGAACGCGCCGTTGCCGACATTGAAACCACAGACGA[T/C]
TGGCGCATCCCACTAATCAAATTCATCAGCAGCGAGGAGTTGCCCAAGGACAATACAGAGGCCGAGAAAATAACCTGTAAAGCAAAGATCTACTGTATGG

Reverse complement sequence

CCATACAGTAGATCTTTGCTTTACAGGTTATTTTCTCGGCCTCTGTATTGTCCTTGGGCAACTCCTCGCTGCTGATGAATTTGATTAGTGGGATGCGCCA[A/G]
TCGTCTGTGGTTTCAATGTCGGCAACGGCGCGTTCTACCTCGGTGACCTCCGAGCTAATGTCGGGGGTGTTCGGGCTGACTTCGCCGCTAACCTCTTTCA

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	47.20%	0.30%	13.84%	38.64%	NA
All Indica	2759	30.60%	0.10%	11.74%	57.59%	NA
All Japonica	1512	84.70%	0.20%	3.37%	11.71%	NA
Aus	269	11.20%	2.20%	74.35%	12.27%	NA
Indica I	595	25.50%	0.00%	14.79%	59.66%	NA
Indica II	465	58.90%	0.20%	6.24%	34.62%	NA
Indica III	913	16.10%	0.20%	11.06%	72.62%	NA
Indica Intermediate	786	34.40%	0.00%	13.49%	52.16%	NA
Temperate Japonica	767	97.70%	0.30%	0.00%	2.09%	NA
Tropical Japonica	504	63.90%	0.20%	7.54%	28.37%	NA
Japonica Intermediate	241	87.10%	0.00%	5.39%	7.47%	NA
VI/Aromatic	96	33.30%	1.00%	65.62%	0.00%	NA
Intermediate	90	50.00%	2.20%	17.78%	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
vg1018461662	T -> C	LOC_Os10g34640.1	synonymous_variant ; p.Asp543Asp; LOW	synonymous_codon	Average:25.255; most accessible tissue: Minghui63 root, score: 36.81	N	N	N	N
vg1018461662	T -> DEL	LOC_Os10g34640.1	N	frameshift_variant	Average:25.255; most accessible tissue: Minghui63 root, score: 36.81	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1018461662	NA	1.50E-07	mr1129	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
vg1018461662	NA	4.00E-10	mr1235	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
vg1018461662	NA	1.94E-07	mr1243	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
vg1018461662	NA	2.00E-06	mr1257	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
vg1018461662	NA	3.31E-08	mr1423	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
vg1018461662	NA	1.05E-10	mr1435	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
vg1018461662	NA	5.97E-07	mr1584	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
vg1018461662	NA	8.21E-09	mr1599	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
vg1018461662	4.97E-06	4.97E-06	mr1748	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
vg1018461662	3.18E-06	3.18E-06	mr1783	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
vg1018461662	NA	4.16E-14	mr1784	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
vg1018461662	NA	1.36E-06	mr1805	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
vg1018461662	NA	7.74E-10	mr1862	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
vg1018461662	NA	1.97E-06	mr1558_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