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Detailed information for vg1004721834:

Variant ID: vg1004721834 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 4721834
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCTCCGTACGAAGCACTGTATGGTCGGAAGTGCCGCACTCCGCTTTTGTGGGATCAAACGGGAGAACGTCAGGTTTTCGGGAAGCAGAAGAGAAGGTAAA[G/C]
ATCATTCAAGAAAGGTTGCGTGTGGCTCAGTCTCGCCATAAGAGTTATGCCGACAATCGCCGCAGAGATTTGAGTTTTGAAGAAGGAGATTATGTGTACC

Reverse complement sequence

GGTACACATAATCTCCTTCTTCAAAACTCAAATCTCTGCGGCGATTGTCGGCATAACTCTTATGGCGAGACTGAGCCACACGCAACCTTTCTTGAATGAT[C/G]
TTTACCTTCTCTTCTGCTTCCCGAAAACCTGACGTTCTCCCGTTTGATCCCACAAAAGCGGAGTGCGGCACTTCCGACCATACAGTGCTTCGTACGGAGC

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	86.60%	2.30%	1.54%	9.54%	NA
All Indica	2759	91.70%	0.30%	1.41%	6.63%	NA
All Japonica	1512	87.80%	6.50%	0.20%	5.49%	NA
Aus	269	23.80%	0.00%	11.15%	65.06%	NA
Indica I	595	80.30%	0.00%	0.50%	19.16%	NA
Indica II	465	94.40%	0.00%	0.43%	5.16%	NA
Indica III	913	95.50%	0.90%	2.19%	1.42%	NA
Indica Intermediate	786	94.10%	0.00%	1.78%	4.07%	NA
Temperate Japonica	767	95.20%	0.10%	0.00%	4.69%	NA
Tropical Japonica	504	79.80%	19.00%	0.00%	1.19%	NA
Japonica Intermediate	241	80.90%	0.80%	1.24%	17.01%	NA
VI/Aromatic	96	95.80%	0.00%	1.04%	3.12%	NA
Intermediate	90	88.90%	3.30%	0.00%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1004721834	G -> C	LOC_Os10g08702.1	missense_variant ; p.Lys1101Asn; MODERATE	nonsynonymous_codon ; K1101N	Average:12.562; most accessible tissue: Minghui63 young leaf, score: 32.638	possibly damaging	1.918	DELETERIOUS	0.00
vg1004721834	G -> DEL	LOC_Os10g08702.1	N	frameshift_variant	Average:12.562; most accessible tissue: Minghui63 young leaf, score: 32.638	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1004721834	2.83E-06	NA	mr1817	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