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Detailed information for vg1005050526:

Variant ID: vg1005050526 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 5050526
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTCTTGGTTACCCCGCACATACTCGTGGCTATCGTGTACTTATTTTAGGGACTAACAAAATTGTTGGGACTTGCGAAGTTTCTTTTGATGAGGCTAGTCC[T/A]
GGTACTAGACTCGATATTGCAGGTACACTGTCACAGGTTCAGGGGGAGGATGGTCGTATTTTTGAAGACGAGAGCGACTACGACGACGACGACGAGGTCG

Reverse complement sequence

CGACCTCGTCGTCGTCGTCGTAGTCGCTCTCGTCTTCAAAAATACGACCATCCTCCCCCTGAACCTGTGACAGTGTACCTGCAATATCGAGTCTAGTACC[A/T]
GGACTAGCCTCATCAAAAGAAACTTCGCAAGTCCCAACAATTTTGTTAGTCCCTAAAATAAGTACACGATAGCCACGAGTATGTGCGGGGTAACCAAGAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	35.70%	0.10%	47.14%	17.01%	NA
All Indica	2759	19.00%	0.20%	67.27%	13.59%	NA
All Japonica	1512	68.40%	0.00%	8.60%	23.02%	NA
Aus	269	14.50%	0.00%	63.20%	22.30%	NA
Indica I	595	42.00%	0.00%	46.05%	11.93%	NA
Indica II	465	16.10%	0.00%	65.16%	18.71%	NA
Indica III	913	4.30%	0.20%	86.09%	9.42%	NA
Indica Intermediate	786	20.20%	0.40%	62.72%	16.67%	NA
Temperate Japonica	767	80.10%	0.00%	2.74%	17.21%	NA
Tropical Japonica	504	54.80%	0.00%	15.28%	29.96%	NA
Japonica Intermediate	241	59.80%	0.00%	13.28%	26.97%	NA
VI/Aromatic	96	45.80%	0.00%	46.88%	7.29%	NA
Intermediate	90	54.40%	0.00%	30.00%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1005050526	T -> A	LOC_Os10g09350.1	synonymous_variant ; p.Pro897Pro; LOW	synonymous_codon	Average:11.825; most accessible tissue: Minghui63 root, score: 21.615	N	N	N	N
vg1005050526	T -> DEL	LOC_Os10g09350.1	N	frameshift_variant	Average:11.825; most accessible tissue: Minghui63 root, score: 21.615	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1005050526	NA	2.86E-09	mr1302	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
vg1005050526	NA	2.17E-14	mr1361	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
vg1005050526	NA	8.13E-07	mr1392	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
vg1005050526	NA	2.90E-07	mr1886	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
vg1005050526	3.02E-06	1.56E-08	mr1860_2	Jap_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
vg1005050526	NA	3.60E-06	mr1866_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