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Detailed information for vg1104325526:

Variant ID: vg1104325526 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 4325526
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GATGACTGGGCTCTCAGCCCCGCCGGAGCCTACTGCAAGGATGGCTCCGGCAATGTCAGGGACAGCTGCTGCTGCCGTCCCAATGCGACCGTCGCCGTCG[A/T]
CGACGACGTCGACCACCATCGCCGTATCCACCTTCACCAGCTCGATCTCCGTCGTTGATCGTTGATTGATTACGTACTACCTGAGTGATGATGGACGTGG

Reverse complement sequence

CCACGTCCATCATCACTCAGGTAGTACGTAATCAATCAACGATCAACGACGGAGATCGAGCTGGTGAAGGTGGATACGGCGATGGTGGTCGACGTCGTCG[T/A]
CGACGGCGACGGTCGCATTGGGACGGCAGCAGCAGCTGTCCCTGACATTGCCGGAGCCATCCTTGCAGTAGGCTCCGGCGGGGCTGAGAGCCCAGTCATC

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	88.80%	0.50%	6.58%	4.13%	NA
All Indica	2759	83.00%	0.80%	9.64%	6.56%	NA
All Japonica	1512	98.10%	0.00%	1.39%	0.53%	NA
Aus	269	91.80%	0.40%	6.32%	1.49%	NA
Indica I	595	97.30%	0.70%	1.68%	0.34%	NA
Indica II	465	67.10%	1.50%	18.92%	12.47%	NA
Indica III	913	86.20%	0.30%	8.21%	5.26%	NA
Indica Intermediate	786	78.00%	0.90%	11.83%	9.29%	NA
Temperate Japonica	767	99.70%	0.00%	0.13%	0.13%	NA
Tropical Japonica	504	95.40%	0.00%	3.37%	1.19%	NA
Japonica Intermediate	241	98.30%	0.00%	1.24%	0.41%	NA
VI/Aromatic	96	97.90%	1.00%	1.04%	0.00%	NA
Intermediate	90	90.00%	1.10%	6.67%	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
vg1104325526	A -> T	LOC_Os11g08230.1	missense_variant ; p.Val7Asp; MODERATE	nonsynonymous_codon ; V7D	Average:60.027; most accessible tissue: Minghui63 panicle, score: 74.563	unknown	unknown	DELETERIOUS	0.00
vg1104325526	A -> T	LOC_Os11g08235.1	missense_variant ; p.Asp129Val; MODERATE	nonsynonymous_codon ; D129V	Average:60.027; most accessible tissue: Minghui63 panicle, score: 74.563	unknown	unknown	TOLERATED	0.22
vg1104325526	A -> DEL	LOC_Os11g08230.1	N	frameshift_variant	Average:60.027; most accessible tissue: Minghui63 panicle, score: 74.563	N	N	N	N
vg1104325526	A -> DEL	LOC_Os11g08235.1	N	frameshift_variant	Average:60.027; most accessible tissue: Minghui63 panicle, score: 74.563	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1104325526	8.20E-06	NA	mr1127	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
vg1104325526	2.84E-08	1.59E-10	mr1218	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
vg1104325526	NA	6.41E-08	mr1583	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
vg1104325526	NA	1.25E-06	mr1622	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
vg1104325526	NA	9.48E-06	mr1622	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
vg1104325526	3.75E-17	1.04E-55	mr1638	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
vg1104325526	3.40E-10	2.79E-13	mr1638	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
vg1104325526	NA	2.93E-07	mr1638	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
vg1104325526	9.82E-07	5.27E-06	mr1695	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
vg1104325526	NA	5.15E-09	mr1218_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
vg1104325526	NA	3.48E-09	mr1850_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