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Detailed information for vg1004355426:

Variant ID: vg1004355426 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 4355426
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAAGTTGGGCACCTCAAATCCTTGCGGGTATGGGACTGAATCTACGTGTTCAGGATACGGCCTTTGGTATGTATGCATAGCTACTTTCGATTCTATTTCA[C/G]
TACTATCCCGCAAGACATTGTCATCATCTTTCCCAACATCCACATGACCGATTTGTGATTCGGTCTTAGGTGATAATGCTATTTCACTTTCGCTTGTGAT

Reverse complement sequence

ATCACAAGCGAAAGTGAAATAGCATTATCACCTAAGACCGAATCACAAATCGGTCATGTGGATGTTGGGAAAGATGATGACAATGTCTTGCGGGATAGTA[G/C]
TGAAATAGAATCGAAAGTAGCTATGCATACATACCAAAGGCCGTATCCTGAACACGTAGATTCAGTCCCATACCCGCAAGGATTTGAGGTGCCCAACTTC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	69.40%	0.60%	3.68%	26.34%	NA
All Indica	2759	70.80%	0.70%	3.70%	24.86%	NA
All Japonica	1512	61.20%	0.70%	3.44%	34.72%	NA
Aus	269	99.30%	0.00%	0.00%	0.74%	NA
Indica I	595	64.70%	0.00%	1.68%	33.61%	NA
Indica II	465	74.80%	0.20%	1.94%	23.01%	NA
Indica III	913	76.10%	0.80%	6.46%	16.65%	NA
Indica Intermediate	786	66.70%	1.40%	3.05%	28.88%	NA
Temperate Japonica	767	84.40%	0.00%	0.13%	15.51%	NA
Tropical Japonica	504	22.80%	1.80%	8.53%	66.87%	NA
Japonica Intermediate	241	67.60%	0.40%	3.32%	28.63%	NA
VI/Aromatic	96	71.90%	0.00%	9.38%	18.75%	NA
Intermediate	90	72.20%	0.00%	12.22%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1004355426	C -> G	LOC_Os10g08030.1	missense_variant ; p.Ser55Thr; MODERATE	nonsynonymous_codon ; S55T	Average:26.769; most accessible tissue: Zhenshan97 flag leaf, score: 39.027	benign	0.244	TOLERATED	0.99
vg1004355426	C -> DEL	LOC_Os10g08030.1	N	frameshift_variant	Average:26.769; most accessible tissue: Zhenshan97 flag leaf, score: 39.027	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1004355426	2.47E-06	2.47E-06	mr1661	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
vg1004355426	NA	3.43E-06	mr1077_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