RiceVarMap2

Detailed information for vg1105974431:

Variant ID: vg1105974431 (JBrowse)

Variation Type: SNP

Chromosome: chr11

Position: 5974431

Reference Allele: C

Alternative Allele: T

Primary Allele: C

Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGCCGGCGAGCACCGCGGCAGCTCGGTGACGGCGAAGGGCCGCATCGACATGGACGCCGGGGAGCGCGAGTCGGTGGTGATCGGCGGCACGGGGCGGTTT[C/T]
GGCTCGCGCGCGGGTACATGGTCACCAAGAACTACGACTACAGCCTCGCCACCGGCGGCGTCGTCCAGATCGACGTCTGCCTGCAGCACTAGCTAGCCAT

Reverse complement sequence

ATGGCTAGCTAGTGCTGCAGGCAGACGTCGATCTGGACGACGCCGCCGGTGGCGAGGCTGTAGTCGTAGTTCTTGGTGACCATGTACCCGCGCGCGAGCC[G/A]
AAACCGCCCCGTGCCGCCGATCACCACCGACTCGCGCTCCCCGGCGTCCATGTCGATGCGGCCCTTCGCCGTCACCGAGCTGCCGCGGTGCTCGCCGGCC

Allele Frequencies:

Search:

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	38.10%	2.60%	10.22%	49.05%	NA
All Indica	2759	29.90%	0.80%	10.15%	59.15%	NA
All Japonica	1512	56.70%	6.60%	10.38%	26.32%	NA
Aus	269	12.60%	0.00%	11.90%	75.46%	NA
Indica I	595	30.90%	0.00%	17.31%	51.76%	NA
Indica II	465	22.60%	0.20%	11.18%	66.02%	NA
Indica III	913	29.80%	1.80%	4.82%	63.64%	NA
Indica Intermediate	786	33.60%	0.60%	10.31%	55.47%	NA
Temperate Japonica	767	56.50%	2.10%	12.26%	29.20%	NA
Tropical Japonica	504	52.80%	13.30%	7.74%	26.19%	NA
Japonica Intermediate	241	65.60%	7.10%	9.96%	17.43%	NA
VI/Aromatic	96	39.60%	0.00%	6.25%	54.17%	NA
Intermediate	90	51.10%	3.30%	8.89%	36.67%	NA

Showing 1 to 13 of 13 entries

Allele Effect:

Search:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1105974431	C -> T	LOC_Os11g10840.1	missense_variant ; p.Arg38Trp; MODERATE	nonsynonymous_codon ; R38W	Average:33.674; most accessible tissue: Callus, score: 75.127	probably damaging	3.66	DELETERIOUS	0.00
vg1105974431	C -> DEL	LOC_Os11g10840.1	N	frameshift_variant	Average:33.674; most accessible tissue: Callus, score: 75.127	N	N	N	N

Showing 1 to 2 of 2 entries

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Detailed information for vg1105974431:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

RiceVarMap v2.0

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