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Detailed information for vg0413260405:

Variant ID: vg0413260405 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 13260405
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAGGCCCCAAGCAACCTGGTAACGACATCGATGTATACATAAGACCACTAGTCGAAGATCTTAAACTGTTATGGAAGAAGGAAGGTGTTCCCGTGTGGGA[C/T]
GAGGACAAACAGGAGGAGTTTAACCTACGAGCACTGCTGTTCGTAACCATCAACGATTGGCCTACACTTAGCAACCTATCCGGGCAGTCCAATAAGGGGT

Reverse complement sequence

ACCCCTTATTGGACTGCCCGGATAGGTTGCTAAGTGTAGGCCAATCGTTGATGGTTACGAACAGCAGTGCTCGTAGGTTAAACTCCTCCTGTTTGTCCTC[G/A]
TCCCACACGGGAACACCTTCCTTCTTCCATAACAGTTTAAGATCTTCGACTAGTGGTCTTATGTATACATCGATGTCGTTACCAGGTTGCTTGGGGCCTT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	82.90%	12.20%	1.23%	3.68%	NA
All Indica	2759	89.30%	2.50%	1.92%	6.23%	NA
All Japonica	1512	67.40%	32.30%	0.20%	0.07%	NA
Aus	269	99.30%	0.00%	0.37%	0.37%	NA
Indica I	595	95.30%	0.00%	1.18%	3.53%	NA
Indica II	465	96.30%	1.50%	0.86%	1.29%	NA
Indica III	913	80.90%	4.10%	3.29%	11.72%	NA
Indica Intermediate	786	90.30%	3.30%	1.53%	4.83%	NA
Temperate Japonica	767	90.50%	9.30%	0.13%	0.13%	NA
Tropical Japonica	504	26.20%	73.40%	0.40%	0.00%	NA
Japonica Intermediate	241	80.10%	19.90%	0.00%	0.00%	NA
VI/Aromatic	96	91.70%	8.30%	0.00%	0.00%	NA
Intermediate	90	86.70%	12.20%	1.11%	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
vg0413260405	C -> DEL	LOC_Os04g23240.1	N	frameshift_variant	Average:25.475; most accessible tissue: Minghui63 flag leaf, score: 42.036	N	N	N	N
vg0413260405	C -> T	LOC_Os04g23240.1	synonymous_variant ; p.Asp422Asp; LOW	synonymous_codon	Average:25.475; most accessible tissue: Minghui63 flag leaf, score: 42.036	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0413260405	NA	9.34E-07	mr1029	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
vg0413260405	NA	5.41E-10	mr1047	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
vg0413260405	NA	7.19E-06	mr1047	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
vg0413260405	NA	4.08E-09	mr1089	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
vg0413260405	2.41E-06	3.07E-08	mr1189	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
vg0413260405	4.43E-06	NA	mr1471	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
vg0413260405	NA	2.17E-07	mr1471	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
vg0413260405	NA	6.14E-08	mr1625	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
vg0413260405	NA	3.21E-10	mr1642	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
vg0413260405	NA	2.30E-06	mr1642	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
vg0413260405	NA	2.74E-07	mr1782	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
vg0413260405	NA	8.99E-07	mr1796	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
vg0413260405	NA	2.57E-08	mr1990	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
vg0413260405	NA	1.54E-09	mr1642_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