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Detailed information for vg1009824904:

Variant ID: vg1009824904 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 9824904
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCAGTGTCCACCCACCAATTAGGTGAGTGAAAAACAGAGAGAACTGTAGGTAATATTTTACCGCACCCCGATGTTCCTCCGCCCTCGCTAATAACCATGT[T/C]
GGCAGACTTCCTGTCTTTGCGCTCAGGACAGTCCTTGGCCCAATGCCCAGACTTGCCACACACAAAGCAGTCTCCCTTTGCCTTTCCCTTGCCTTTCTTC

Reverse complement sequence

GAAGAAAGGCAAGGGAAAGGCAAAGGGAGACTGCTTTGTGTGTGGCAAGTCTGGGCATTGGGCCAAGGACTGTCCTGAGCGCAAAGACAGGAAGTCTGCC[A/G]
ACATGGTTATTAGCGAGGGCGGAGGAACATCGGGGTGCGGTAAAATATTACCTACAGTTCTCTCTGTTTTTCACTCACCTAATTGGTGGGTGGACACTGG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	16.20%	0.20%	33.62%	49.92%	NA
All Indica	2759	4.90%	0.30%	30.55%	64.26%	NA
All Japonica	1512	40.10%	0.00%	28.24%	31.68%	NA
Aus	269	1.50%	0.70%	72.86%	24.91%	NA
Indica I	595	5.20%	0.70%	57.65%	36.47%	NA
Indica II	465	6.20%	0.00%	13.98%	79.78%	NA
Indica III	913	3.10%	0.10%	19.72%	77.11%	NA
Indica Intermediate	786	6.00%	0.40%	32.44%	61.20%	NA
Temperate Japonica	767	60.00%	0.00%	23.99%	16.04%	NA
Tropical Japonica	504	12.30%	0.00%	40.67%	47.02%	NA
Japonica Intermediate	241	34.90%	0.00%	15.77%	49.38%	NA
VI/Aromatic	96	5.20%	0.00%	89.58%	5.21%	NA
Intermediate	90	18.90%	1.10%	41.11%	38.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1009824904	T -> C	LOC_Os10g19290.1	missense_variant ; p.Asn418Asp; MODERATE	nonsynonymous_codon	Average:11.974; most accessible tissue: Callus, score: 18.646	possibly damaging	1.634	DELETERIOUS	0.00
vg1009824904	T -> DEL	LOC_Os10g19290.1	N	frameshift_variant	Average:11.974; most accessible tissue: Callus, score: 18.646	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1009824904	4.87E-06	4.87E-06	mr1173	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
vg1009824904	NA	5.44E-06	mr1789	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