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Detailed information for vg0403617354:

Variant ID: vg0403617354 (JBrowse)	Variation Type: INDEL
Chromosome: chr04	Position: 3617354
Reference Allele: TA	Alternative Allele: CA,TAA,T,TAAA,AA
Primary Allele: CA	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACGTGGCGCCCACGTGGCGGTGTTGACCAAGTCTTTATCCTACGTGGCGCTTACGTGGCATTAGAATTAAAAAATATGTGAAACCCATATGCCATTCACA[TA/CA,TAA,T,TAAA,AA]
AAAAAAAGAGTATTGTAGGATCCACTGACAAGTGGGACCCACATGTCATCCTCCCTCTCCTTCCCTTCTTCCTCTCCTCTCTCTCCCTTATCTCTCTCCC

Reverse complement sequence

GGGAGAGAGATAAGGGAGAGAGAGGAGAGGAAGAAGGGAAGGAGAGGGAGGATGACATGTGGGTCCCACTTGTCAGTGGATCCTACAATACTCTTTTTTT[TA/TG,TTA,A,TTTA,TT]
TGTGAATGGCATATGGGTTTCACATATTTTTTAATTCTAATGCCACGTAAGCGCCACGTAGGATAAAGACTTGGTCAACACCGCCACGTGGGCGCCACGT

Allele Frequencies:

Populations	Population Size	Frequency of CA(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	43.10%	9.80%	2.60%	35.70%	TA: 7.15%; TAA: 1.08%; TAAA: 0.49%; AA: 0.11%
All Indica	2759	53.60%	0.80%	1.34%	39.00%	TA: 4.20%; TAAA: 0.76%; TAA: 0.18%; AA: 0.04%
All Japonica	1512	33.10%	27.30%	5.09%	16.93%	TA: 14.22%; TAA: 3.04%; AA: 0.20%; TAAA: 0.07%
Aus	269	5.60%	1.10%	1.12%	92.19%	NA
Indica I	595	96.00%	0.00%	0.50%	3.19%	TA: 0.34%
Indica II	465	57.40%	1.50%	3.01%	31.18%	TA: 5.81%; TAAA: 0.65%; TAA: 0.43%
Indica III	913	24.30%	0.90%	0.33%	66.48%	TA: 6.68%; TAAA: 1.10%; TAA: 0.11%; AA: 0.11%
Indica Intermediate	786	53.40%	1.00%	2.16%	38.80%	TA: 3.31%; TAAA: 1.02%; TAA: 0.25%
Temperate Japonica	767	51.90%	6.50%	8.74%	2.61%	TA: 24.64%; TAA: 5.61%
Tropical Japonica	504	11.30%	59.70%	1.19%	24.80%	TA: 2.18%; AA: 0.60%; TAAA: 0.20%
Japonica Intermediate	241	19.10%	25.70%	1.66%	46.06%	TA: 6.22%; TAA: 1.24%
VI/Aromatic	96	4.20%	8.30%	1.04%	86.46%	NA
Intermediate	90	40.00%	17.80%	5.56%	26.67%	TA: 7.78%; AA: 1.11%; TAAA: 1.11%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0403617354	TA -> CA	LOC_Os04g06860.1	missense_variant ; p.Met159Val; MODERATE	nonsynonymous_codon ; M159V	Average:60.686; most accessible tissue: Zhenshan97 young leaf, score: 79.225	unknown	unknown	unknown	unknown
vg0403617354	TA -> DEL	LOC_Os04g06860.1	N	frameshift_variant	Average:60.686; most accessible tissue: Zhenshan97 young leaf, score: 79.225	N	N	N	N
vg0403617354	TA -> AA	LOC_Os04g06860.1	missense_variant ; p.Met159Leu; MODERATE	nonsynonymous_codon ; M159L	Average:60.686; most accessible tissue: Zhenshan97 young leaf, score: 79.225	unknown	unknown	unknown	unknown
vg0403617354	TA -> TAA	LOC_Os04g06860.1	frameshift_variant ; p.Met159fs; HIGH	frameshift_variant	Average:60.686; most accessible tissue: Zhenshan97 young leaf, score: 79.225	N	N	N	N
vg0403617354	TA -> TAAA	LOC_Os04g06860.1	frameshift_variant ; p.Met159fs; HIGH	frameshift_variant	Average:60.686; most accessible tissue: Zhenshan97 young leaf, score: 79.225	N	N	N	N
vg0403617354	TA -> T	LOC_Os04g06860.1	frameshift_variant ; p.Phe158fs; HIGH	frameshift_variant	Average:60.686; most accessible tissue: Zhenshan97 young leaf, score: 79.225	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0403617354	NA	9.72E-07	mr1208	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
vg0403617354	NA	6.54E-07	mr1619	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
vg0403617354	4.55E-06	NA	mr1071_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
vg0403617354	5.62E-08	NA	mr1080_2	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
vg0403617354	3.57E-06	NA	mr1203_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
vg0403617354	8.49E-07	6.22E-08	mr1619_2	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