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Detailed information for vg0137283220:

Variant ID: vg0137283220 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 37283220
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATTTTGTGAATGAGGTATTAAAAAATTTATTATTTGAATATATCATTCAGAAAACATTAAGATTAATAAAAAAGATCAAAAAATCATTATGTTGAATTT[T/C]
ACATGAGTGCAGGTTGAACAAAATGGAAATGATTCTATGCAGACTGTCATTGATGCAAAAAAATATGTCTGAGGTGATTCCAGAAATGAATTTTGAAGCT

Reverse complement sequence

AGCTTCAAAATTCATTTCTGGAATCACCTCAGACATATTTTTTTGCATCAATGACAGTCTGCATAGAATCATTTCCATTTTGTTCAACCTGCACTCATGT[A/G]
AAATTCAACATAATGATTTTTTGATCTTTTTTATTAATCTTAATGTTTTCTGAATGATATATTCAAATAATAAATTTTTTAATACCTCATTCACAAAATT

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	92.90%	2.20%	4.23%	0.74%	NA
All Indica	2759	99.90%	0.00%	0.04%	0.04%	NA
All Japonica	1512	78.50%	6.50%	12.83%	2.12%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.00%	0.13%	0.13%	NA
Temperate Japonica	767	79.50%	1.30%	17.21%	1.96%	NA
Tropical Japonica	504	83.90%	7.50%	6.15%	2.38%	NA
Japonica Intermediate	241	63.90%	21.20%	12.86%	2.07%	NA
VI/Aromatic	96	95.80%	0.00%	3.12%	1.04%	NA
Intermediate	90	94.40%	2.20%	2.22%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0137283220	T -> DEL	N	N	silent_mutation	Average:14.059; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N
vg0137283220	T -> C	LOC_Os01g64190.1	upstream_gene_variant ; 2729.0bp to feature; MODIFIER	silent_mutation	Average:14.059; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N
vg0137283220	T -> C	LOC_Os01g64200.1	intron_variant ; MODIFIER	silent_mutation	Average:14.059; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0137283220	NA	3.10E-08	mr1117	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
vg0137283220	NA	2.66E-06	mr1118	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
vg0137283220	NA	4.71E-06	mr1180	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
vg0137283220	NA	7.12E-08	mr1240	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
vg0137283220	NA	3.89E-09	mr1496	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
vg0137283220	NA	1.13E-07	mr1693	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
vg0137283220	NA	9.41E-09	mr1117_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
vg0137283220	NA	1.23E-06	mr1118_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
vg0137283220	NA	1.32E-06	mr1119_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
vg0137283220	1.86E-06	1.85E-06	mr1197_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
vg0137283220	NA	2.04E-06	mr1240_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
vg0137283220	NA	6.45E-06	mr1242_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
vg0137283220	NA	1.25E-09	mr1496_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