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Detailed information for vg1127000154:

Variant ID: vg1127000154 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 27000154
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACGATTGATTCCTGTTATAAAAACGGGGGTCCACACCAATAGAGGGGGAACCAAGCAAAGCGGACGAGGGAGGTGAGGTCGATCAGCTGCGCATAGACAA[C/T]
GTCTCCACAGCTTGTGCCGAGGGCAGGGAGCTGGAGAAGAGCTACGAGAGCGTGATGACGTGGTCCAGTGAGAGGGGCTGGGCGAAGAAGGCGTTGTAGG

Reverse complement sequence

CCTACAACGCCTTCTTCGCCCAGCCCCTCTCACTGGACCACGTCATCACGCTCTCGTAGCTCTTCTCCAGCTCCCTGCCCTCGGCACAAGCTGTGGAGAC[G/A]
TTGTCTATGCGCAGCTGATCGACCTCACCTCCCTCGTCCGCTTTGCTTGGTTCCCCCTCTATTGGTGTGGACCCCCGTTTTTATAACAGGAATCAATCGT

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	68.50%	26.70%	0.55%	4.34%	NA
All Indica	2759	76.50%	16.80%	0.69%	5.98%	NA
All Japonica	1512	58.00%	40.90%	0.26%	0.86%	NA
Aus	269	40.90%	50.90%	0.74%	7.43%	NA
Indica I	595	73.30%	25.20%	0.84%	0.67%	NA
Indica II	465	79.40%	18.50%	0.86%	1.29%	NA
Indica III	913	75.10%	11.10%	0.66%	13.14%	NA
Indica Intermediate	786	78.90%	16.20%	0.51%	4.45%	NA
Temperate Japonica	767	74.40%	24.60%	0.26%	0.65%	NA
Tropical Japonica	504	40.30%	58.50%	0.00%	1.19%	NA
Japonica Intermediate	241	42.70%	55.60%	0.83%	0.83%	NA
VI/Aromatic	96	83.30%	12.50%	0.00%	4.17%	NA
Intermediate	90	63.30%	32.20%	1.11%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1127000154	C -> T	LOC_Os11g44650.1	synonymous_variant ; p.Asn40Asn; LOW	synonymous_codon	Average:44.935; most accessible tissue: Minghui63 young leaf, score: 71.254	N	N	N	N
vg1127000154	C -> DEL	LOC_Os11g44650.1	N	frameshift_variant	Average:44.935; most accessible tissue: Minghui63 young leaf, score: 71.254	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1127000154	1.52E-08	2.36E-08	mr1538_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