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Detailed information for vg1010574400:

Variant ID: vg1010574400 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 10574400
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTACATGATTACATAGTAATATACTCCCTTCATTCCAAATTGATCTGCTTATAGTTTTTTTTGAGATTATTACTAAATGATCTATATATTTGTGTTCATT[T/C]
ATTAAGTCTATTCGTTATTTGTGCATTAGAGTAAATGGACATTGATGCATGCATCCATGCACACAAGTATTTATAACCCACATGTAATATCTTGATTTGC

Reverse complement sequence

GCAAATCAAGATATTACATGTGGGTTATAAATACTTGTGTGCATGGATGCATGCATCAATGTCCATTTACTCTAATGCACAAATAACGAATAGACTTAAT[A/G]
AATGAACACAAATATATAGATCATTTAGTAATAATCTCAAAAAAAACTATAAGCAGATCAATTTGGAATGAAGGGAGTATATTACTATGTAATCATGTAA

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	50.70%	22.20%	0.87%	26.24%	NA
All Indica	2759	77.90%	1.10%	0.54%	20.44%	NA
All Japonica	1512	13.20%	64.30%	1.19%	21.36%	NA
Aus	269	1.90%	1.10%	2.23%	94.80%	NA
Indica I	595	95.60%	1.00%	0.00%	3.36%	NA
Indica II	465	88.20%	0.90%	0.65%	10.32%	NA
Indica III	913	64.40%	1.30%	0.55%	33.73%	NA
Indica Intermediate	786	74.20%	1.00%	0.89%	23.92%	NA
Temperate Japonica	767	15.10%	80.70%	0.13%	4.04%	NA
Tropical Japonica	504	4.20%	48.20%	2.58%	45.04%	NA
Japonica Intermediate	241	25.70%	45.60%	1.66%	26.97%	NA
VI/Aromatic	96	6.20%	14.60%	1.04%	78.12%	NA
Intermediate	90	38.90%	34.40%	1.11%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1010574400	T -> C	LOC_Os10g20860.1	upstream_gene_variant ; 411.0bp to feature; MODIFIER	silent_mutation	Average:31.052; most accessible tissue: Zhenshan97 root, score: 41.416	N	N	N	N
vg1010574400	T -> C	LOC_Os10g20870.1	downstream_gene_variant ; 600.0bp to feature; MODIFIER	silent_mutation	Average:31.052; most accessible tissue: Zhenshan97 root, score: 41.416	N	N	N	N
vg1010574400	T -> C	LOC_Os10g20880.1	downstream_gene_variant ; 3410.0bp to feature; MODIFIER	silent_mutation	Average:31.052; most accessible tissue: Zhenshan97 root, score: 41.416	N	N	N	N
vg1010574400	T -> C	LOC_Os10g20860-LOC_Os10g20870	intergenic_region ; MODIFIER	silent_mutation	Average:31.052; most accessible tissue: Zhenshan97 root, score: 41.416	N	N	N	N
vg1010574400	T -> DEL	N	N	silent_mutation	Average:31.052; most accessible tissue: Zhenshan97 root, score: 41.416	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1010574400	NA	2.31E-06	mr1111	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
vg1010574400	NA	4.70E-06	mr1120_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
vg1010574400	4.03E-07	2.09E-07	mr1258_2	Ind_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