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Detailed information for vg0605135820:

Variant ID: vg0605135820 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 5135820
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTAGAGAGAACGTTGGACTTCCTTTGTCAGCCTCGTGCGGGCACCGAAAGGGTTTGTCTAAGTCAATCTCTGATGTCGACCGAGAAAGTATAGAGCGTA[C/T]
GACTAAGTCTCCCGTCTTGCTGTAATCGAGAATTTGGATTGAAGTCAAGAAATTTTATCTCGGCGGGTACACAATTTCTTCATTCCGTATTCCTTTTCGA

Reverse complement sequence

TCGAAAAGGAATACGGAATGAAGAAATTGTGTACCCGCCGAGATAAAATTTCTTGACTTCAATCCAAATTCTCGATTACAGCAAGACGGGAGACTTAGTC[G/A]
TACGCTCTATACTTTCTCGGTCGACATCAGAGATTGACTTAGACAAACCCTTTCGGTGCCCGCACGAGGCTGACAAAGGAAGTCCAACGTTCTCTCTAAA

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	76.00%	20.10%	0.40%	3.49%	NA
All Indica	2759	91.60%	2.20%	0.58%	5.69%	NA
All Japonica	1512	43.50%	56.10%	0.13%	0.26%	NA
Aus	269	92.60%	7.10%	0.37%	0.00%	NA
Indica I	595	80.70%	1.20%	1.01%	17.14%	NA
Indica II	465	96.60%	1.90%	0.43%	1.08%	NA
Indica III	913	95.80%	0.80%	0.44%	2.96%	NA
Indica Intermediate	786	91.90%	4.70%	0.51%	2.93%	NA
Temperate Japonica	767	44.10%	55.80%	0.13%	0.00%	NA
Tropical Japonica	504	40.70%	58.70%	0.00%	0.60%	NA
Japonica Intermediate	241	47.70%	51.50%	0.41%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	70.00%	25.60%	0.00%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0605135820	C -> T	LOC_Os06g10090.1	downstream_gene_variant ; 1348.0bp to feature; MODIFIER	silent_mutation	Average:17.69; most accessible tissue: Minghui63 young leaf, score: 31.294	N	N	N	N
vg0605135820	C -> T	LOC_Os06g10070-LOC_Os06g10090	intergenic_region ; MODIFIER	silent_mutation	Average:17.69; most accessible tissue: Minghui63 young leaf, score: 31.294	N	N	N	N
vg0605135820	C -> DEL	N	N	silent_mutation	Average:17.69; most accessible tissue: Minghui63 young leaf, score: 31.294	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0605135820	2.25E-06	NA	mr1178	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