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Detailed information for vg1105183431:

Variant ID: vg1105183431 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 5183431
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.03, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:

ACTTGACGTACCAGAGATGGCTAAAACATATGAGCAAGTCACTGGTTTTGAGCTTGGGAAAGAACCCCCGGAGGAGTTGTTTGAGACGTACGACAACTGC[T/C]
CTCTCATTATGGAAGTTGTTAAAGCTCATGGGATTTCTTTTCTCCTTGGAGAATATGATACCTTGCTTCAAAATAAGTGTGTTGATTTACCTCCAATCCC

Reverse complement sequence

GGGATTGGAGGTAAATCAACACACTTATTTTGAAGCAAGGTATCATATTCTCCAAGGAGAAAAGAAATCCCATGAGCTTTAACAACTTCCATAATGAGAG[A/G]
GCAGTTGTCGTACGTCTCAAACAACTCCTCCGGGGGTTCTTTCCCAAGCTCAAAACCAGTGACTTGCTCATATGTTTTAGCCATCTCTGGTACGTCAAGT

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	57.70%	9.70%	0.34%	32.23%	NA
All Indica	2759	48.90%	0.70%	0.47%	49.98%	NA
All Japonica	1512	70.90%	27.80%	0.00%	1.32%	NA
Aus	269	65.40%	1.10%	0.74%	32.71%	NA
Indica I	595	23.90%	2.20%	0.84%	73.11%	NA
Indica II	465	19.40%	0.20%	0.86%	79.57%	NA
Indica III	913	73.10%	0.00%	0.22%	26.73%	NA
Indica Intermediate	786	57.30%	0.50%	0.25%	41.98%	NA
Temperate Japonica	767	64.40%	33.20%	0.00%	2.35%	NA
Tropical Japonica	504	85.90%	14.10%	0.00%	0.00%	NA
Japonica Intermediate	241	60.20%	39.00%	0.00%	0.83%	NA
VI/Aromatic	96	85.40%	4.20%	1.04%	9.38%	NA
Intermediate	90	54.40%	15.60%	0.00%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1105183431	T -> DEL	LOC_Os11g09710.1	N	frameshift_variant	Average:17.689; most accessible tissue: Callus, score: 92.298	N	N	N	N
vg1105183431	T -> C	LOC_Os11g09710.1	missense_variant ; p.Ser169Pro; MODERATE	nonsynonymous_codon ; S169P	Average:17.689; most accessible tissue: Callus, score: 92.298	possibly damaging	-1.531	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1105183431	6.79E-06	6.79E-06	mr1957_2	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