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Detailed information for vg0505172195:

Variant ID: vg0505172195 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 5172195
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAATGGAAGAGGAGATGTGTCTGGTAGACTGTTGTACCACCAATACTATCTTTTGAGATACCACGTATTTCCAGACTTTAAAGAAAAAGACTGGTCAAAT[C/T]
GCTACTATTGCCGGAAGCAATGCACCCATCGTCGGAGTGGGACGAGCAACAGTAGTTCTCCCACATGGTACCAAGATCATTATAAATGATGCTCTATTAT

Reverse complement sequence

ATAATAGAGCATCATTTATAATGATCTTGGTACCATGTGGGAGAACTACTGTTGCTCGTCCCACTCCGACGATGGGTGCATTGCTTCCGGCAATAGTAGC[G/A]
ATTTGACCAGTCTTTTTCTTTAAAGTCTGGAAATACGTGGTATCTCAAAAGATAGTATTGGTGGTACAACAGTCTACCAGACACATCTCCTCTTCCATTG

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	83.80%	2.80%	5.01%	8.42%	NA
All Indica	2759	95.00%	0.20%	3.41%	1.41%	NA
All Japonica	1512	72.30%	7.90%	8.13%	11.71%	NA
Aus	269	33.50%	0.00%	4.83%	61.71%	NA
Indica I	595	92.30%	0.00%	7.73%	0.00%	NA
Indica II	465	93.30%	0.90%	3.23%	2.58%	NA
Indica III	913	99.20%	0.10%	0.33%	0.33%	NA
Indica Intermediate	786	93.00%	0.10%	3.82%	3.05%	NA
Temperate Japonica	767	70.50%	15.30%	10.04%	4.17%	NA
Tropical Japonica	504	74.80%	0.00%	6.94%	18.25%	NA
Japonica Intermediate	241	72.60%	0.80%	4.56%	21.99%	NA
VI/Aromatic	96	95.80%	0.00%	1.04%	3.12%	NA
Intermediate	90	73.30%	5.60%	6.67%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0505172195	C -> T	LOC_Os05g09260.1	upstream_gene_variant ; 1129.0bp to feature; MODIFIER	silent_mutation	Average:31.758; most accessible tissue: Minghui63 flag leaf, score: 48.324	N	N	N	N
vg0505172195	C -> T	LOC_Os05g09270.1	upstream_gene_variant ; 2194.0bp to feature; MODIFIER	silent_mutation	Average:31.758; most accessible tissue: Minghui63 flag leaf, score: 48.324	N	N	N	N
vg0505172195	C -> T	LOC_Os05g09250.1	downstream_gene_variant ; 395.0bp to feature; MODIFIER	silent_mutation	Average:31.758; most accessible tissue: Minghui63 flag leaf, score: 48.324	N	N	N	N
vg0505172195	C -> T	LOC_Os05g09250-LOC_Os05g09260	intergenic_region ; MODIFIER	silent_mutation	Average:31.758; most accessible tissue: Minghui63 flag leaf, score: 48.324	N	N	N	N
vg0505172195	C -> DEL	N	N	silent_mutation	Average:31.758; most accessible tissue: Minghui63 flag leaf, score: 48.324	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0505172195	1.36E-06	1.36E-06	mr1955	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
vg0505172195	NA	2.29E-06	mr1588_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