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Detailed information for vg0413765723:

Variant ID: vg0413765723 (JBrowse)	Variation Type: INDEL
Chromosome: chr04	Position: 13765723
Reference Allele: GT	Alternative Allele: AT,G
Primary Allele: GT	Secondary Allele: AT

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAATGCCACCCGCCACAAACTTGTCCGGCAACTCACAGTTGTTGTTCTCAAGTTCCTTAGCCAGCATCTGAATCTCATGAGCTTGTTCTACTACAGAACG[GT/AT,G]
CATCGACCATCTTGTAGTCATAGAACTGCTCCATGACATACAGCTCACTGCCGGTGTCAGAAACTCCGAACTTGGCCTCAAGTGCATCCCACATGTCCTT

Reverse complement sequence

AAGGACATGTGGGATGCACTTGAGGCCAAGTTCGGAGTTTCTGACACCGGCAGTGAGCTGTATGTCATGGAGCAGTTCTATGACTACAAGATGGTCGATG[AC/AT,C]
CGTTCTGTAGTAGAACAAGCTCATGAGATTCAGATGCTGGCTAAGGAACTTGAGAACAACAACTGTGAGTTGCCGGACAAGTTTGTGGCGGGTGGCATTA

Allele Frequencies:

Populations	Population Size	Frequency of GT(primary allele)	Frequency of AT(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	94.00%	5.40%	0.61%	0.00%	NA
All Indica	2759	96.40%	3.20%	0.40%	0.00%	NA
All Japonica	1512	91.70%	7.50%	0.79%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	88.60%	10.60%	0.84%	0.00%	NA
Indica II	465	99.10%	0.20%	0.65%	0.00%	NA
Indica III	913	99.60%	0.30%	0.11%	0.00%	NA
Indica Intermediate	786	96.90%	2.80%	0.25%	0.00%	NA
Temperate Japonica	767	98.30%	1.70%	0.00%	0.00%	NA
Tropical Japonica	504	87.70%	10.30%	1.98%	0.00%	NA
Japonica Intermediate	241	79.30%	19.90%	0.83%	0.00%	NA
VI/Aromatic	96	52.10%	43.80%	4.17%	0.00%	NA
Intermediate	90	86.70%	11.10%	2.22%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0413765723	GT -> G	LOC_Os04g24100.1	frameshift_variant ; p.Asp271fs; HIGH	N	Average:33.701; most accessible tissue: Zhenshan97 flower, score: 61.872	N	N	N	N
vg0413765723	GT -> AT	LOC_Os04g24100.1	synonymous_variant ; p.Asp271Asp; LOW	synonymous_codon	Average:33.701; most accessible tissue: Zhenshan97 flower, score: 61.872	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0413765723	5.07E-06	NA	mr1584	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
vg0413765723	1.34E-07	4.69E-10	mr1350_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
vg0413765723	1.21E-07	NA	mr1368_2	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
vg0413765723	1.10E-06	NA	mr1584_2	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
vg0413765723	5.21E-12	NA	mr1730_2	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
vg0413765723	3.60E-07	6.99E-08	mr1730_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
vg0413765723	8.93E-07	NA	mr1853_2	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
vg0413765723	1.27E-09	NA	mr1866_2	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