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Detailed information for vg1219872223:

Variant ID: vg1219872223 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 19872223
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CATGTGCCTCCTGAATTCATTGAAAAGCCTGTCGAGAACGAAGAACGGTATTTGGTTATCGACCAGGAGGAGGTCGTAGTATATGCTGTTCGACATCAAC[T/C]
GCATGTGATTGTCGACATGGGCATGGTCTCCCTCTCTCCACTGGAGGAGGAGCTCGACGATGAAGCACCCGTCACGCGTGAGCATGTCCGCGGTGTACAA

Reverse complement sequence

TTGTACACCGCGGACATGCTCACGCGTGACGGGTGCTTCATCGTCGAGCTCCTCCTCCAGTGGAGAGAGGGAGACCATGCCCATGTCGACAATCACATGC[A/G]
GTTGATGTCGAACAGCATATACTACGACCTCCTCCTGGTCGATAACCAAATACCGTTCTTCGTTCTCGACAGGCTTTTCAATGAATTCAGGAGGCACATG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	68.60%	8.20%	4.04%	19.15%	NA
All Indica	2759	67.40%	0.30%	1.16%	31.10%	NA
All Japonica	1512	64.40%	24.30%	9.59%	1.72%	NA
Aus	269	95.20%	0.00%	1.12%	3.72%	NA
Indica I	595	74.10%	0.20%	2.02%	23.70%	NA
Indica II	465	62.40%	1.10%	0.65%	35.91%	NA
Indica III	913	67.00%	0.00%	0.00%	32.97%	NA
Indica Intermediate	786	65.80%	0.40%	2.16%	31.68%	NA
Temperate Japonica	767	40.70%	45.80%	13.17%	0.39%	NA
Tropical Japonica	504	90.90%	0.40%	4.76%	3.97%	NA
Japonica Intermediate	241	84.60%	5.80%	8.30%	1.24%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	64.40%	12.20%	12.22%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1219872223	T -> C	LOC_Os12g32880.1	missense_variant ; p.Gln115Arg; MODERATE	nonsynonymous_codon ; Q115R	Average:51.739; most accessible tissue: Callus, score: 79.057	unknown	unknown	TOLERATED	1.00
vg1219872223	T -> DEL	LOC_Os12g32880.1	N	frameshift_variant	Average:51.739; most accessible tissue: Callus, score: 79.057	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1219872223	NA	1.07E-06	mr1163	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
vg1219872223	NA	6.96E-10	mr1486	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
vg1219872223	NA	6.38E-23	mr1010_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
vg1219872223	NA	4.94E-13	mr1010_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
vg1219872223	NA	8.40E-10	mr1011_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
vg1219872223	NA	4.13E-07	mr1011_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
vg1219872223	NA	6.98E-07	mr1013_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
vg1219872223	NA	1.12E-07	mr1137_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
vg1219872223	1.07E-08	NA	mr1486_2	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
vg1219872223	9.50E-07	4.62E-15	mr1486_2	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
vg1219872223	NA	3.01E-06	mr1588_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
vg1219872223	NA	1.45E-06	mr1617_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