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Detailed information for vg1005136400:

Variant ID: vg1005136400 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 5136400
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CATCAAGGATTATGATGTGGAAATTCACTATCATCCTGGTAACGGAACCCTATGGAACGGAAATCGGGTATGCGTTCCGGATAACAGGGAACTTAAACAG[C/T]
TGATACTTCAGGAAGCTCACGAAAGTCCTTATTCCATCCACCCTGGCAGTACGAAGATGTACTTAGACTTGAAGGAGAAATACTGGTGGGTTAGTATGAA

Reverse complement sequence

TTCATACTAACCCACCAGTATTTCTCCTTCAAGTCTAAGTACATCTTCGTACTGCCAGGGTGGATGGAATAAGGACTTTCGTGAGCTTCCTGAAGTATCA[G/A]
CTGTTTAAGTTCCCTGTTATCCGGAACGCATACCCGATTTCCGTTCCATAGGGTTCCGTTACCAGGATGATAGTGAATTTCCACATCATAATCCTTGATG

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	97.00%	0.10%	2.37%	0.55%	NA
All Indica	2759	97.00%	0.00%	2.46%	0.51%	NA
All Japonica	1512	96.50%	0.20%	2.51%	0.79%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	96.50%	0.00%	3.53%	0.00%	NA
Indica II	465	95.30%	0.00%	2.80%	1.94%	NA
Indica III	913	97.90%	0.00%	1.75%	0.33%	NA
Indica Intermediate	786	97.50%	0.00%	2.29%	0.25%	NA
Temperate Japonica	767	94.50%	0.00%	4.04%	1.43%	NA
Tropical Japonica	504	98.20%	0.60%	0.99%	0.20%	NA
Japonica Intermediate	241	99.20%	0.00%	0.83%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	94.40%	0.00%	5.56%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1005136400	C -> T	LOC_Os10g09510.1	synonymous_variant ; p.Leu381Leu; LOW	synonymous_codon	Average:20.023; most accessible tissue: Callus, score: 34.682	N	N	N	N
vg1005136400	C -> DEL	LOC_Os10g09510.1	N	frameshift_variant	Average:20.023; most accessible tissue: Callus, score: 34.682	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1005136400	1.99E-06	1.99E-06	mr1649_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
vg1005136400	NA	7.94E-06	mr1884_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