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Detailed information for vg0721415417:

Variant ID: vg0721415417 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 21415417
Reference Allele: G	Alternative Allele: T
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.73, G: 0.27, others allele: 0.00, population size: 84. )

Flanking Sequence (100 bp) in Reference Genome:

TGTCTGCATCTAGCAAGACGTTGCTCGCCTTCATGTCACGGTGGATGATCTTCTTCTGTGAGTCCTGGTGAAGATATTGTAGTCCTCTAGCAATGCCTTC[G/T]
ATGATCTTGAATCGTGTTGCCCAATCAAGTTGTCTGCTTTGCTCCGAGTCTAATTGACACGTGATGAAGAGATTATTGTAATTATTGCATGTCAGCAAAC

Reverse complement sequence

GTTTGCTGACATGCAATAATTACAATAATCTCTTCATCACGTGTCAATTAGACTCGGAGCAAAGCAGACAACTTGATTGGGCAACACGATTCAAGATCAT[C/A]
GAAGGCATTGCTAGAGGACTACAATATCTTCACCAGGACTCACAGAAGAAGATCATCCACCGTGACATGAAGGCGAGCAACGTCTTGCTAGATGCAGACA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	62.10%	19.20%	8.93%	9.82%	NA
All Indica	2759	59.80%	11.00%	13.63%	15.55%	NA
All Japonica	1512	76.20%	23.70%	0.07%	0.00%	NA
Aus	269	17.50%	59.50%	12.27%	10.78%	NA
Indica I	595	26.40%	3.20%	30.92%	39.50%	NA
Indica II	465	72.70%	15.10%	3.66%	8.60%	NA
Indica III	913	69.10%	15.70%	8.87%	6.35%	NA
Indica Intermediate	786	66.80%	9.00%	11.96%	12.21%	NA
Temperate Japonica	767	68.10%	31.90%	0.00%	0.00%	NA
Tropical Japonica	504	89.30%	10.70%	0.00%	0.00%	NA
Japonica Intermediate	241	74.70%	24.90%	0.41%	0.00%	NA
VI/Aromatic	96	35.40%	58.30%	6.25%	0.00%	NA
Intermediate	90	54.40%	32.20%	6.67%	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
vg0721415417	G -> DEL	LOC_Os07g35750.1	N	frameshift_variant	Average:35.318; most accessible tissue: Minghui63 root, score: 69.344	N	N	N	N
vg0721415417	G -> DEL	LOC_Os07g35750.2	N	frameshift_variant	Average:35.318; most accessible tissue: Minghui63 root, score: 69.344	N	N	N	N
vg0721415417	G -> T	LOC_Os07g35750.1	synonymous_variant ; p.Ile453Ile; LOW	synonymous_codon	Average:35.318; most accessible tissue: Minghui63 root, score: 69.344	N	N	N	N
vg0721415417	G -> T	LOC_Os07g35750.2	synonymous_variant ; p.Ile453Ile; LOW	synonymous_codon	Average:35.318; most accessible tissue: Minghui63 root, score: 69.344	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0721415417	4.70E-06	NA	mr1218	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