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Detailed information for vg0906483706:

Variant ID: vg0906483706 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 6483706
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTGCGGTCCTTGTGATTGTTACTTCCACCCTCTCCCGTAGTCGGCGCATCTTTCTTTGGCTTCCAAGTAGGACCCAACTGCTTGGATGCGGCAATGGCGT[T/C]
TTCGTCTTTGGCATACTCATTGGCTTTTTCAAACATCTGTTTGACTGTCTTGGGAGGTTTGCGCCCGAACTTGCCGACTAGTTCTTCGTGATGAATTCCT

Reverse complement sequence

AGGAATTCATCACGAAGAACTAGTCGGCAAGTTCGGGCGCAAACCTCCCAAGACAGTCAAACAGATGTTTGAAAAAGCCAATGAGTATGCCAAAGACGAA[A/G]
ACGCCATTGCCGCATCCAAGCAGTTGGGTCCTACTTGGAAGCCAAAGAAAGATGCGCCGACTACGGGAGAGGGTGGAAGTAACAATCACAAGGACCGCAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	53.30%	5.70%	5.37%	35.67%	NA
All Indica	2759	26.40%	5.40%	8.41%	59.84%	NA
All Japonica	1512	99.40%	0.10%	0.00%	0.46%	NA
Aus	269	61.00%	30.90%	4.09%	4.09%	NA
Indica I	595	32.80%	0.30%	3.03%	63.87%	NA
Indica II	465	27.10%	7.10%	7.96%	57.85%	NA
Indica III	913	15.80%	7.40%	15.33%	61.45%	NA
Indica Intermediate	786	33.50%	5.70%	4.71%	56.11%	NA
Temperate Japonica	767	99.70%	0.00%	0.00%	0.26%	NA
Tropical Japonica	504	99.20%	0.20%	0.00%	0.60%	NA
Japonica Intermediate	241	98.80%	0.40%	0.00%	0.83%	NA
VI/Aromatic	96	60.40%	30.20%	9.38%	0.00%	NA
Intermediate	90	71.10%	7.80%	2.22%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0906483706	T -> DEL	LOC_Os09g11610.1	N	frameshift_variant	Average:31.062; most accessible tissue: Minghui63 flag leaf, score: 64.867	N	N	N	N
vg0906483706	T -> C	LOC_Os09g11610.1	missense_variant ; p.Asn188Asp; MODERATE	nonsynonymous_codon	Average:31.062; most accessible tissue: Minghui63 flag leaf, score: 64.867	unknown	unknown	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0906483706	NA	7.72E-06	mr1125	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
vg0906483706	8.79E-06	NA	mr1260	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