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Detailed information for vg0721414343:

Variant ID: vg0721414343 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 21414343
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTACACATATATTACGCAAGTTTCACAATCTCCTCATAAGATGAGTTTGTATTATTTCCAAAATTTGTAGTCAAGAAAATTCATTTTCCTATAATCGATG[A/T]
AACAGGATGAAGCTCTGCTAAGGAGTACTTGGACCTATCCAACCCATATAGTATGTTAAATGTGATGGATCAAATGTCCTCATAGAATTTCGCTTTCTTT

Reverse complement sequence

AAAGAAAGCGAAATTCTATGAGGACATTTGATCCATCACATTTAACATACTATATGGGTTGGATAGGTCCAAGTACTCCTTAGCAGAGCTTCATCCTGTT[T/A]
CATCGATTATAGGAAAATGAATTTTCTTGACTACAAATTTTGGAAATAATACAAACTCATCTTATGAGGAGATTGTGAAACTTGCGTAATATATGTGTAA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	91.10%	2.20%	1.25%	5.42%	NA
All Indica	2759	96.20%	2.50%	1.27%	0.07%	NA
All Japonica	1512	82.50%	0.00%	0.79%	16.67%	NA
Aus	269	82.20%	13.40%	4.46%	0.00%	NA
Indica I	595	95.30%	2.20%	2.52%	0.00%	NA
Indica II	465	97.40%	1.70%	0.65%	0.22%	NA
Indica III	913	98.60%	0.70%	0.77%	0.00%	NA
Indica Intermediate	786	93.40%	5.20%	1.27%	0.13%	NA
Temperate Japonica	767	69.20%	0.00%	1.17%	29.60%	NA
Tropical Japonica	504	98.80%	0.00%	0.20%	0.99%	NA
Japonica Intermediate	241	90.90%	0.00%	0.83%	8.30%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	0.00%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0721414343	A -> DEL	N	N	silent_mutation	Average:51.12; most accessible tissue: Zhenshan97 flower, score: 74.459	N	N	N	N
vg0721414343	A -> T	LOC_Os07g35750.1	3_prime_UTR_variant ; 235.0bp to feature; MODIFIER	silent_mutation	Average:51.12; most accessible tissue: Zhenshan97 flower, score: 74.459	N	N	N	N
vg0721414343	A -> T	LOC_Os07g35750.2	3_prime_UTR_variant ; 882.0bp to feature; MODIFIER	silent_mutation	Average:51.12; most accessible tissue: Zhenshan97 flower, score: 74.459	N	N	N	N
vg0721414343	A -> T	LOC_Os07g35740.1	upstream_gene_variant ; 2656.0bp to feature; MODIFIER	silent_mutation	Average:51.12; most accessible tissue: Zhenshan97 flower, score: 74.459	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0721414343	3.44E-06	NA	mr1598	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