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Detailed information for vg0123776609:

Variant ID: vg0123776609 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 23776609
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAATGGCTAGAACTCCAGTTCATCCACGATCGTCCTCGATTGTAGCTGCATTCACTTACCTTTTGCTAGTCCTCTTCCGAGACGCCATCACCACCGCAGC[T/C]
GCATCTCCCAAAGCTCCGGCATCCACCAATGGCTGCATTGCAGCCGAGAGGGATGCCCTGCTCTCGTTCAAGGCTGGCATCACAAGAGACCCCAAGAAAC

Reverse complement sequence

GTTTCTTGGGGTCTCTTGTGATGCCAGCCTTGAACGAGAGCAGGGCATCCCTCTCGGCTGCAATGCAGCCATTGGTGGATGCCGGAGCTTTGGGAGATGC[A/G]
GCTGCGGTGGTGATGGCGTCTCGGAAGAGGACTAGCAAAAGGTAAGTGAATGCAGCTACAATCGAGGACGATCGTGGATGAACTGGAGTTCTAGCCATTC

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	43.60%	16.00%	22.41%	18.05%	NA
All Indica	2759	9.90%	25.70%	35.09%	29.32%	NA
All Japonica	1512	92.10%	1.90%	3.90%	2.18%	NA
Aus	269	92.20%	1.90%	4.09%	1.86%	NA
Indica I	595	2.70%	19.00%	55.29%	23.03%	NA
Indica II	465	6.20%	23.40%	35.70%	34.62%	NA
Indica III	913	11.20%	34.90%	22.45%	31.43%	NA
Indica Intermediate	786	16.20%	21.20%	34.10%	28.50%	NA
Temperate Japonica	767	99.50%	0.10%	0.13%	0.26%	NA
Tropical Japonica	504	79.00%	5.00%	10.12%	5.95%	NA
Japonica Intermediate	241	95.90%	0.80%	2.90%	0.41%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	56.70%	14.40%	22.22%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0123776609	T -> DEL	LOC_Os01g41930.1	N	frameshift_variant	Average:70.595; most accessible tissue: Minghui63 root, score: 85.252	N	N	N	N
vg0123776609	T -> C	LOC_Os01g41930.1	synonymous_variant ; p.Ala36Ala; LOW	synonymous_codon	Average:70.595; most accessible tissue: Minghui63 root, score: 85.252	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0123776609	NA	3.27E-07	mr1850	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
vg0123776609	NA	1.25E-06	mr1870_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