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Detailed information for vg1005078438:

Variant ID: vg1005078438 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 5078438
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACATGTTCTCCCTGGCCCATATATGCTGCTACATAGCCTGACCAGCCGCCTATGCTCTTGGTCTTGAAGTCATATTTGTTCTTTGTATTCAAACTCATAG[G/C]
GTTGGCCGATGAGGTGACATCCAGACCCGTGATCATGCTGATATCTATGAGAGTTGGGGTCATCGGCCCTTGATTAAACAAAAAGGCATTGATGGTGTTT

Reverse complement sequence

AAACACCATCAATGCCTTTTTGTTTAATCAAGGGCCGATGACCCCAACTCTCATAGATATCAGCATGATCACGGGTCTGGATGTCACCTCATCGGCCAAC[C/G]
CTATGAGTTTGAATACAAAGAACAAATATGACTTCAAGACCAAGAGCATAGGCGGCTGGTCAGGCTATGTAGCAGCATATATGGGCCAGGGAGAACATGT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	36.10%	0.60%	20.10%	43.19%	NA
All Indica	2759	16.90%	0.80%	27.08%	55.24%	NA
All Japonica	1512	71.20%	0.10%	5.82%	22.88%	NA
Aus	269	29.00%	0.40%	28.62%	42.01%	NA
Indica I	595	29.70%	0.20%	21.01%	49.08%	NA
Indica II	465	12.70%	0.90%	23.23%	63.23%	NA
Indica III	913	7.90%	1.50%	33.63%	56.96%	NA
Indica Intermediate	786	20.10%	0.40%	26.34%	53.18%	NA
Temperate Japonica	767	79.70%	0.00%	4.82%	15.51%	NA
Tropical Japonica	504	62.70%	0.00%	7.94%	29.37%	NA
Japonica Intermediate	241	62.20%	0.40%	4.56%	32.78%	NA
VI/Aromatic	96	43.80%	4.20%	25.00%	27.08%	NA
Intermediate	90	47.80%	1.10%	15.56%	35.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1005078438	G -> C	LOC_Os10g09410.1	missense_variant ; p.Pro166Ala; MODERATE	nonsynonymous_codon ; P166A	Average:18.373; most accessible tissue: Callus, score: 28.606	possibly damaging	1.728	DELETERIOUS	0.01
vg1005078438	G -> DEL	LOC_Os10g09410.1	N	frameshift_variant	Average:18.373; most accessible tissue: Callus, score: 28.606	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1005078438	2.13E-06	2.13E-06	mr1370	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
vg1005078438	1.16E-06	1.15E-06	mr1370	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