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Detailed information for vg0721100662:

Variant ID: vg0721100662 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 21100662
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACGGCTGGCCTATTATGCCACCGTTGTTGGGCGTCTACGTCTTCACTGACCGGCCGCCTCGTCCGCCGCCGACTGGTGTTTCCGCCTGCACGGTTGGCCT[A/C]
TTATGCCGCCGTTGTTGGGCGTCTATGTCTTCACCGACCGGCTTGCCCTCGTCCGCCGCCGACTGGTGTTTCCGCCTGCACGGCTGGCCTGTTATGACAC

Reverse complement sequence

GTGTCATAACAGGCCAGCCGTGCAGGCGGAAACACCAGTCGGCGGCGGACGAGGGCAAGCCGGTCGGTGAAGACATAGACGCCCAACAACGGCGGCATAA[T/G]
AGGCCAACCGTGCAGGCGGAAACACCAGTCGGCGGCGGACGAGGCGGCCGGTCAGTGAAGACGTAGACGCCCAACAACGGTGGCATAATAGGCCAGCCGT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	73.20%	3.10%	6.26%	17.41%	NA
All Indica	2759	59.60%	5.30%	9.97%	25.19%	NA
All Japonica	1512	92.50%	0.10%	1.12%	6.35%	NA
Aus	269	93.70%	0.40%	0.74%	5.20%	NA
Indica I	595	50.40%	0.00%	10.76%	38.82%	NA
Indica II	465	54.60%	3.70%	9.46%	32.26%	NA
Indica III	913	67.80%	10.70%	10.30%	11.17%	NA
Indica Intermediate	786	59.80%	3.90%	9.29%	26.97%	NA
Temperate Japonica	767	99.20%	0.00%	0.00%	0.78%	NA
Tropical Japonica	504	82.70%	0.00%	1.59%	15.67%	NA
Japonica Intermediate	241	91.30%	0.40%	3.73%	4.56%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	78.90%	0.00%	2.22%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0721100662	A -> DEL	LOC_Os07g35250.1	N	frameshift_variant	Average:10.551; most accessible tissue: Minghui63 root, score: 17.665	N	N	N	N
vg0721100662	A -> C	LOC_Os07g35250.1	missense_variant ; p.Asn92Lys; MODERATE	nonsynonymous_codon	Average:10.551; most accessible tissue: Minghui63 root, score: 17.665	benign	0.677	DELETERIOUS	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0721100662	5.34E-06	5.34E-06	mr1473	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
vg0721100662	6.65E-06	6.65E-06	mr1664	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