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Detailed information for vg0901405183:

Variant ID: vg0901405183 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 1405183
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACTGGTAGCAGGGAACAAAAAGAGCTCTCTTCCTTGCAGTAAGATGAACCCTGGCCTTCTGTGGTGGCGCTTCTCCCTTCAATTCGGCCAGTTCCTTCTC[T/C]
AGACGATCAACCTTGTCCTCTAGCTTGCAAATCTTACCACGGTTCCAATCTTCACGAGCTTGAGCAGCTGACACAACTTCAGCGCGGGACTCATCCATGG

Reverse complement sequence

CCATGGATGAGTCCCGCGCTGAAGTTGTGTCAGCTGCTCAAGCTCGTGAAGATTGGAACCGTGGTAAGATTTGCAAGCTAGAGGACAAGGTTGATCGTCT[A/G]
GAGAAGGAACTGGCCGAATTGAAGGGAGAAGCGCCACCACAGAAGGCCAGGGTTCATCTTACTGCAAGGAAGAGAGCTCTTTTTGTTCCCTGCTACCAGT

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	80.80%	5.90%	3.53%	9.73%	NA
All Indica	2759	98.10%	1.20%	0.58%	0.14%	NA
All Japonica	1512	49.90%	16.10%	6.02%	28.04%	NA
Aus	269	99.30%	0.40%	0.00%	0.37%	NA
Indica I	595	99.20%	0.20%	0.50%	0.17%	NA
Indica II	465	93.80%	5.60%	0.43%	0.22%	NA
Indica III	913	99.30%	0.20%	0.44%	0.00%	NA
Indica Intermediate	786	98.30%	0.50%	0.89%	0.25%	NA
Temperate Japonica	767	80.30%	13.40%	4.82%	1.43%	NA
Tropical Japonica	504	8.90%	19.40%	7.74%	63.89%	NA
Japonica Intermediate	241	38.60%	17.40%	6.22%	37.76%	NA
VI/Aromatic	96	24.00%	0.00%	51.04%	25.00%	NA
Intermediate	90	76.70%	3.30%	12.22%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0901405183	T -> DEL	LOC_Os09g02990.1	N	frameshift_variant	Average:40.406; most accessible tissue: Zhenshan97 flag leaf, score: 67.785	N	N	N	N
vg0901405183	T -> C	LOC_Os09g02990.1	synonymous_variant ; p.Leu253Leu; LOW	synonymous_codon	Average:40.406; most accessible tissue: Zhenshan97 flag leaf, score: 67.785	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0901405183	2.75E-06	2.75E-06	mr1908_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