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Detailed information for vg1011221880:

Variant ID: vg1011221880 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 11221880
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 327. )

Flanking Sequence (100 bp) in Reference Genome:

TATCAGGCATAGTCCAATCGGCTACAAAGTCGGCAAGTACCTGGGACTTGATGGCTGTTCGTGGCACAAAGCGGACATCAAATTGGCTTAGCTCGACTAC[C/A]
CATTTCGCGATGCGGCCGACAACGTCTTTGTTTCTCACTACTTCACCGAGAGGGAAAGAGGATACAACTGTGACCCTGTGGGCTTCGAAGTAGTGGCGTA

Reverse complement sequence

TACGCCACTACTTCGAAGCCCACAGGGTCACAGTTGTATCCTCTTTCCCTCTCGGTGAAGTAGTGAGAAACAAAGACGTTGTCGGCCGCATCGCGAAATG[G/T]
GTAGTCGAGCTAAGCCAATTTGATGTCCGCTTTGTGCCACGAACAGCCATCAAGTCCCAGGTACTTGCCGACTTTGTAGCCGATTGGACTATGCCTGATA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	78.50%	14.60%	2.20%	4.72%	NA
All Indica	2759	92.20%	3.60%	2.75%	1.41%	NA
All Japonica	1512	48.70%	37.80%	1.79%	11.64%	NA
Aus	269	99.60%	0.00%	0.00%	0.37%	NA
Indica I	595	87.70%	5.40%	5.21%	1.68%	NA
Indica II	465	98.90%	0.40%	0.65%	0.00%	NA
Indica III	913	90.30%	4.10%	3.29%	2.41%	NA
Indica Intermediate	786	93.90%	3.70%	1.53%	0.89%	NA
Temperate Japonica	767	80.80%	18.90%	0.00%	0.26%	NA
Tropical Japonica	504	7.50%	56.20%	4.76%	31.55%	NA
Japonica Intermediate	241	32.80%	59.80%	1.24%	6.22%	NA
VI/Aromatic	96	92.70%	6.20%	0.00%	1.04%	NA
Intermediate	90	78.90%	13.30%	1.11%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1011221880	C -> A	LOC_Os10g21830.1	missense_variant ; p.Trp208Cys; MODERATE	nonsynonymous_codon ; W208C	Average:50.711; most accessible tissue: Minghui63 flag leaf, score: 79.383	probably damaging	3.682	DELETERIOUS	0.02
vg1011221880	C -> DEL	LOC_Os10g21830.1	N	frameshift_variant	Average:50.711; most accessible tissue: Minghui63 flag leaf, score: 79.383	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1011221880	7.55E-07	NA	mr1071	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
vg1011221880	2.37E-06	NA	mr1140	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
vg1011221880	4.27E-06	NA	mr1203	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
vg1011221880	NA	3.23E-07	mr1310	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
vg1011221880	NA	1.42E-10	mr1354	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
vg1011221880	8.50E-06	NA	mr1395	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
vg1011221880	NA	1.06E-10	mr1580	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
vg1011221880	4.95E-06	NA	mr1618	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
vg1011221880	NA	5.96E-08	mr1825	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
vg1011221880	5.40E-06	NA	mr1203_2	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
vg1011221880	NA	6.38E-11	mr1354_2	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
vg1011221880	NA	4.25E-07	mr1768_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