TraceHaplotyper
uploaded_file1 -> d3258_3012R.ab1
uploaded_file2 -> tra16R.exp
action -> phase
RESULTS
In the expected sequence the deletion is after base 200, indel size 8 bases.
SNP1 is at base 212, alleles A and G.
In the trace file the deletion site detected at position 188, score 640.1 (lower than 600 may indicate low trace file quality)
hence, to align the expected and the trace sequences a -12-base difference is accounted for.
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Analysis for SNP1, alleles A and G
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Finding the SNP1 allele that is located on the Ins chromosome
The expected pair of bases before the SNP site is G C
In the trace, the pairs of bases are:
190 base1 T base2 C
191 base1 C base2 G
192 base1 G base2 A are in the expected SNP site
193 base1 C base2 G
194 base1 A base2 T
The pair of bases that should precede the site of SNP on the Ins chromosome was located at 0 bases from the expected position
hence, the site of SNP for the Ins chromosome is at position 192 base1 G base2 A of these the expected base for the Del chromosome is G
Haplotype 1 is: Del, A
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Finding the SNP1 allele that is located on the Del chromosome
The expected pair of bases before the SNP site is G C
In the trace, the pairs of bases are:
198 base1 T base2 C
199 base1 G base2 C
200 base1 G base2 T are in the expected SNP site
201 base1 T base2 C
202 base1 G base2 A
The pair of bases that should precede the site of SNP on the Del chromosome was located at 0 bases from the expected position
hence, the site of SNP for the Del chromosome is at position 200 base1 G base2 T of these the expected base for the Ins chromosome is T
Haplotype 2 is: Ins, G
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View trace with
ChromatogramApplet by Eugen Buehler
Eyal Seroussi Ph. D.
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